Code Context //Afterwards, we iterate over the string backwards (starting from the closed bracket character ')') in order to find the corresponding opening bracket,
//and then parse the content between the opening and closing bracket to find all the associated species.
if(preg_match_all("/[)][A-Z][A-Z,a-z,0-9,_]*:/",$newick_species_tree,$matches)){
$newick_species_tree = array(
'result' => '((((((((((((((((((((((((((aly:0.05,ath:0.05)Arabidopsis:0.05,cru:0.05)Camelineae:0.05,chi:0.05):0.05,((((bca:0.05,bol:0.05):0.05,bna:0.05,bra:0.05)Brassica:0.05,spa:0.05):0.05,esa:0.05):0.05):0.05,aar:0.05)Brassicaceae:0.05,tha:0.05):0.05,cpa:0.05)Brassicales:0.05,((col:0.05,tca:0.05):0.05,((ghi:0.05,gra:0.05)Gossypium:0.05,dzi:0.05):0.05)Malvaceae:0.05):0.05,(acertr:0.05,ccl:0.05)Sapindales:0.05):0.05,(egr:0.05,pgr:0.05)Myrtales:0.05)Malvids:0.05,(((((((cav:0.05,cfa:0.05)Betulaceae:0.05,cil:0.05):0.05,qlo:0.05)Fagales:0.05,(((cme:0.05,csa:0.05)Cucumis:0.05,cla:0.05)Benincaseae:0.05,sed:0.05)Cucurbitaceae:0.05):0.05,((((fan:0.05,fve:0.05)Fragaria:0.05,rch:0.05)Rosoideae:0.05,(mdo:0.05,ppe:0.05)Amygdaloideae:0.05)Rosaceae:0.05,cansat:0.05)Rosales:0.05):0.05,(((((((mtr:0.05,tpr:0.05)Trifolieae:0.05,psa:0.05):0.05,car:0.05)IRL_clade:0.05,lja:0.05)Hologalegina:0.05,(gma:0.05,(pvu:0.05,vmu:0.05):0.05)Phaseoleae:0.05)NPAAA_clade:0.05,lal:0.05):0.05,arhy:0.05):0.05):0.05,(((mes:0.05,shi:0.05):0.05,(ptr:0.05,sbr:0.05)Saliceae:0.05)Malpighiales:0.05,twi:0.05):0.05)Fabids:0.05):0.05,vvi:0.05)Rosids:0.05,((((((rsi:0.05,vma:0.05)Ericaceae:0.05,ach:0.05):0.05,camsi:0.05)Ericales:0.05,(din:0.05,hma:0.05)Cornales:0.05):0.05,((((((egut:0.05,sas:0.05):0.05,sbo:0.05):0.05,(ugi:0.05,ama:0.05):0.05):0.05,oeu:0.05)Lamiales:0.05,((((can:0.05,((sly:0.05,spe:0.05):0.05,stu:0.05)Solanum:0.05)Solanoideae:0.05,nta:0.05):0.05,pax:0.05)Solanaceae:0.05,ccan:0.05):0.05)Lamiids:0.05,(((eca:0.05,han:0.05)Asteroideae:0.05,lsa:0.05)Asteraceae:0.05,(dca:0.05,lonja:0.05):0.05)Campanulids:0.05):0.05)Asterids:0.05,((((bvu:0.05,cqu:0.05)Chenopodiaceae:0.05,amhyb:0.05):0.05,sun:0.05):0.05,sci:0.05)Caryophyllales:0.05):0.05)Pentapetalae:0.05,tar:0.05):0.05,nnu:0.05):0.05,(aox:0.05,pso:0.05)Ranunculales:0.05):0.05,cde:0.05):0.05,mbi:0.05):0.05,((osa:0.05,zma:0.05)Poaceae:0.05,vpl:0.05)Liliopsida:0.05)Mesangiospermae:0.05,atr:0.05)Magnoliopsida:0.05,sgi:0.05)Spermatophyta:0.05,smo:0.05)Tracheophyta:0.05,(aag:0.05,(mpo:0.05,ppa:0.05)MossesLiverworts:0.05)Bryophyta:0.05)Embryophyta:0.05,cbr:0.05)Streptophytina:0.05,(cre:0.05,mco:0.05)Chlorophyta:0.05,pco:0.05)Viridiplantae:0.05);'
)
$organism_data = array(
(int) 0 => array(
'species' => 'acertr',
'common_name' => 'Acer truncatum',
'tax_id' => '47965',
'version' => 'v2.0',
'eco_type' => null
),
(int) 1 => array(
'species' => 'ach',
'common_name' => 'Actinidia chinensis',
'tax_id' => '3625',
'version' => 'V3.0',
'eco_type' => null
),
(int) 2 => array(
'species' => 'aar',
'common_name' => 'Aethionema arabicum',
'tax_id' => '228871',
'version' => 'v3.1',
'eco_type' => null
),
(int) 3 => array(
'species' => 'amhyb',
'common_name' => 'Amaranthus hybridus',
'tax_id' => '3565',
'version' => 'v1.0',
'eco_type' => null
),
(int) 4 => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333',
'version' => 'JGI v1.0',
'eco_type' => null
),
(int) 5 => array(
'species' => 'aag',
'common_name' => 'Anthoceros agrestis',
'tax_id' => '41834',
'version' => 'v1.1',
'eco_type' => null
),
(int) 6 => array(
'species' => 'aox',
'common_name' => 'Aquilegia oxysepala',
'tax_id' => '432649',
'version' => 'v1.0',
'eco_type' => 'kansuensis'
),
(int) 7 => array(
'species' => 'aly',
'common_name' => 'Arabidopsis lyrata',
'tax_id' => '59689',
'version' => 'JGI v2.1',
'eco_type' => null
),
(int) 8 => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702',
'version' => 'Araport11',
'eco_type' => 'COL-0'
),
(int) 9 => array(
'species' => 'arhy',
'common_name' => 'Arachis hypogaea',
'tax_id' => '3818',
'version' => 'v1.0',
'eco_type' => 'Tifrunner'
),
(int) 10 => array(
'species' => 'ama',
'common_name' => 'Avicennia marina',
'tax_id' => '82927',
'version' => 'v1.1 20200527',
'eco_type' => null
),
(int) 11 => array(
'species' => 'bvu',
'common_name' => 'Beta vulgaris',
'tax_id' => '161934',
'version' => 'EL10_1.0',
'eco_type' => null
),
(int) 12 => array(
'species' => 'bca',
'common_name' => 'Brassica carinata',
'tax_id' => '52824',
'version' => 'V1.0',
'eco_type' => null
),
(int) 13 => array(
'species' => 'bna',
'common_name' => 'Brassica napus',
'tax_id' => '3708',
'version' => 'v2.0',
'eco_type' => 'Darmor-bzh'
),
(int) 14 => array(
'species' => 'bol',
'common_name' => 'Brassica oleracea',
'tax_id' => '109376',
'version' => 'v1.0',
'eco_type' => 'HDEM'
),
(int) 15 => array(
'species' => 'bra',
'common_name' => 'Brassica rapa',
'tax_id' => '3711',
'version' => 'v1.0',
'eco_type' => 'Z1'
),
(int) 16 => array(
'species' => 'camsi',
'common_name' => 'Camellia sinensis var. sinensis',
'tax_id' => '542762',
'version' => 'CSS_ChrLev_20200506',
'eco_type' => 'Shuchazao'
),
(int) 17 => array(
'species' => 'cansat',
'common_name' => 'Cannabis sativa',
'tax_id' => '3483',
'version' => 'cs10',
'eco_type' => null
),
(int) 18 => array(
'species' => 'cru',
'common_name' => 'Capsella rubella',
'tax_id' => '81985',
'version' => 'JGI v1.1',
'eco_type' => null
),
(int) 19 => array(
'species' => 'can',
'common_name' => 'Capsicum annuum',
'tax_id' => '4072',
'version' => 'Pepper Genome v2.0',
'eco_type' => null
),
(int) 20 => array(
'species' => 'chi',
'common_name' => 'Cardamine hirsuta',
'tax_id' => '50463',
'version' => 'v1.0',
'eco_type' => null
),
(int) 21 => array(
'species' => 'cpa',
'common_name' => 'Carica papaya',
'tax_id' => '3649',
'version' => 'JGI ASGPB0.4',
'eco_type' => null
),
(int) 22 => array(
'species' => 'cfa',
'common_name' => 'Carpinus fangiana',
'tax_id' => '176857',
'version' => 'v1.0',
'eco_type' => null
),
(int) 23 => array(
'species' => 'cil',
'common_name' => 'Carya illinoinensis',
'tax_id' => '32201',
'version' => 'v1.1',
'eco_type' => 'Pawnee'
),
(int) 24 => array(
'species' => 'cde',
'common_name' => 'Ceratophyllum demersum',
'tax_id' => '4428',
'version' => 'v1.0',
'eco_type' => null
),
(int) 25 => array(
'species' => 'cbr',
'common_name' => 'Chara braunii',
'tax_id' => '69332',
'version' => 'Cbr1.0',
'eco_type' => null
),
(int) 26 => array(
'species' => 'cqu',
'common_name' => 'Chenopodium quinoa',
'tax_id' => '63459',
'version' => 'KAUST v1.0',
'eco_type' => null
),
(int) 27 => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055',
'version' => 'JGI v5.5',
'eco_type' => null
),
(int) 28 => array(
'species' => 'car',
'common_name' => 'Cicer arietinum L.',
'tax_id' => '3827',
'version' => 'v3.0',
'eco_type' => 'ICC 4958'
),
(int) 29 => array(
'species' => 'cla',
'common_name' => 'Citrullus lanatus',
'tax_id' => '3654',
'version' => 'WCG v2.0',
'eco_type' => 'Charleston Gray'
),
(int) 30 => array(
'species' => 'ccl',
'common_name' => 'Citrus clementina',
'tax_id' => '85681',
'version' => 'JGI v1.0',
'eco_type' => null
),
(int) 31 => array(
'species' => 'ccan',
'common_name' => 'Coffea canephora',
'tax_id' => '49390',
'version' => 'Coffee Genome Hub v1',
'eco_type' => null
),
(int) 32 => array(
'species' => 'col',
'common_name' => 'Corchorus olitorius',
'tax_id' => '93759',
'version' => 'GenBank v1.0',
'eco_type' => null
),
(int) 33 => array(
'species' => 'cav',
'common_name' => 'Corylus avellana',
'tax_id' => '13451',
'version' => 'v1.0',
'eco_type' => 'Tonda Gentile delle Langhe'
),
(int) 34 => array(
'species' => 'cme',
'common_name' => 'Cucumis melo',
'tax_id' => '3656',
'version' => 'Melonomics v3.6.1',
'eco_type' => null
),
(int) 35 => array(
'species' => 'csa',
'common_name' => 'Cucumis sativus L.',
'tax_id' => '3659',
'version' => 'v3.0',
'eco_type' => 'Chinese Long'
),
(int) 36 => array(
'species' => 'dca',
'common_name' => 'Daucus carota',
'tax_id' => '4039',
'version' => 'JGI v2.0',
'eco_type' => null
),
(int) 37 => array(
'species' => 'din',
'common_name' => 'Davidia involucrata',
'tax_id' => '16924',
'version' => 'v1.0',
'eco_type' => null
),
(int) 38 => array(
'species' => 'dzi',
'common_name' => 'Durio zibethinus',
'tax_id' => '66656',
'version' => 'Duzib1.0',
'eco_type' => null
),
(int) 39 => array(
'species' => 'eca',
'common_name' => 'Erigeron canadensis',
'tax_id' => '72917',
'version' => 'V1.0',
'eco_type' => null
),
(int) 40 => array(
'species' => 'egut',
'common_name' => 'Erythranthe guttata',
'tax_id' => '4155',
'version' => 'v2.0',
'eco_type' => null
),
(int) 41 => array(
'species' => 'egr',
'common_name' => 'Eucalyptus grandis',
'tax_id' => '71139',
'version' => 'v2.0',
'eco_type' => null
),
(int) 42 => array(
'species' => 'esa',
'common_name' => 'Eutrema salsugineum',
'tax_id' => '72664',
'version' => 'v1.0',
'eco_type' => null
),
(int) 43 => array(
'species' => 'fve',
'common_name' => 'Fragaria vesca',
'tax_id' => '57918',
'version' => 'V4.0.a2',
'eco_type' => null
),
(int) 44 => array(
'species' => 'fan',
'common_name' => 'Fragaria x ananassa',
'tax_id' => '3747',
'version' => 'V1.0.a1',
'eco_type' => null
),
(int) 45 => array(
'species' => 'gma',
'common_name' => 'Glycine max',
'tax_id' => '3847',
'version' => 'JGI Wm82.a4.v1',
'eco_type' => null
),
(int) 46 => array(
'species' => 'ghi',
'common_name' => 'Gossypium hirsutum',
'tax_id' => '3635',
'version' => 'v2.1',
'eco_type' => null
),
(int) 47 => array(
'species' => 'gra',
'common_name' => 'Gossypium raimondii',
'tax_id' => '29730',
'version' => 'v2.1',
'eco_type' => null
),
(int) 48 => array(
'species' => 'han',
'common_name' => 'Helianthus annuus',
'tax_id' => '4232',
'version' => 'r1.2',
'eco_type' => null
),
(int) 49 => array(
'species' => 'hma',
'common_name' => 'Hydrangea macrophylla',
'tax_id' => '23110',
'version' => 'v2.1',
'eco_type' => null
),
(int) 50 => array(
'species' => 'lsa',
'common_name' => 'Lactuca sativa',
'tax_id' => '4236',
'version' => 'v8.0',
'eco_type' => null
),
(int) 51 => array(
'species' => 'lonja',
'common_name' => 'Lonicera japonica',
'tax_id' => '105884',
'version' => 'v1.0',
'eco_type' => null
),
(int) 52 => array(
'species' => 'lja',
'common_name' => 'Lotus japonicus',
'tax_id' => '34305',
'version' => 'Lj1.0v1',
'eco_type' => 'MG-20'
),
(int) 53 => array(
'species' => 'lal',
'common_name' => 'Lupinus albus',
'tax_id' => '3870',
'version' => 'v1.0',
'eco_type' => null
),
(int) 54 => array(
'species' => 'mbi',
'common_name' => 'Magnolia biondii',
'tax_id' => '86725',
'version' => 'v1.0',
'eco_type' => null
),
(int) 55 => array(
'species' => 'mdo',
'common_name' => 'Malus domestica',
'tax_id' => '3750',
'version' => 'GDDH13 v1.1',
'eco_type' => null
),
(int) 56 => array(
'species' => 'mes',
'common_name' => 'Manihot esculenta',
'tax_id' => '3983',
'version' => 'v8.1',
'eco_type' => 'Crantz'
),
(int) 57 => array(
'species' => 'mpo',
'common_name' => 'Marchantia polymorpha',
'tax_id' => '3197',
'version' => 'JGI v3.1',
'eco_type' => null
),
(int) 58 => array(
'species' => 'mtr',
'common_name' => 'Medicago truncatula',
'tax_id' => '3880',
'version' => 'JGI Mt4.0v1',
'eco_type' => null
),
(int) 59 => array(
'species' => 'mco',
'common_name' => 'Micromonas commoda',
'tax_id' => '296587',
'version' => 'JGI v3.0',
'eco_type' => null
),
(int) 60 => array(
'species' => 'nnu',
'common_name' => 'Nelumbo nucifera',
'tax_id' => '4432',
'version' => 'v2.0',
'eco_type' => 'China antique'
),
(int) 61 => array(
'species' => 'nta',
'common_name' => 'Nicotiana tabacum',
'tax_id' => '4097',
'version' => 'Edwards2017',
'eco_type' => null
),
(int) 62 => array(
'species' => 'oeu',
'common_name' => 'Olea europaea',
'tax_id' => '4146',
'version' => 'v1.0',
'eco_type' => null
),
(int) 63 => array(
'species' => 'osa',
'common_name' => 'Oryza sativa ssp. japonica',
'tax_id' => '39947',
'version' => 'IRGSP-1.0-2021-05-10',
'eco_type' => null
),
(int) 64 => array(
'species' => 'pso',
'common_name' => 'Papaver somniferum',
'tax_id' => '3469',
'version' => 'ASM357369v1',
'eco_type' => null
),
(int) 65 => array(
'species' => 'pax',
'common_name' => 'Petunia axillaris',
'tax_id' => '33119',
'version' => 'Sol Genomics v1.6.2',
'eco_type' => null
),
(int) 66 => array(
'species' => 'pvu',
'common_name' => 'Phaseolus vulgaris',
'tax_id' => '3885',
'version' => 'v2.1',
'eco_type' => null
),
(int) 67 => array(
'species' => 'ppa',
'common_name' => 'Physcomitrium patens',
'tax_id' => '3218',
'version' => 'JGI v3.3',
'eco_type' => null
),
(int) 68 => array(
'species' => 'psa',
'common_name' => 'Pisum sativum',
'tax_id' => '3888',
'version' => 'V1.0a',
'eco_type' => null
),
(int) 69 => array(
'species' => 'ptr',
'common_name' => 'Populus trichocarpa',
'tax_id' => '3694',
'version' => 'JGI v4.1',
'eco_type' => null
),
(int) 70 => array(
'species' => 'pco',
'common_name' => 'Prasinoderma coloniale',
'tax_id' => '156133',
'version' => 'v1.0',
'eco_type' => null
),
(int) 71 => array(
'species' => 'ppe',
'common_name' => 'Prunus persica',
'tax_id' => '3760',
'version' => 'v2.1',
'eco_type' => null
),
(int) 72 => array(
'species' => 'pgr',
'common_name' => 'Punica granatum',
'tax_id' => '22663',
'version' => 'ASM765513v2',
'eco_type' => null
),
(int) 73 => array(
'species' => 'qlo',
'common_name' => 'Quercus lobata',
'tax_id' => '97700',
'version' => 'v3.0',
'eco_type' => null
),
(int) 74 => array(
'species' => 'rsi',
'common_name' => 'Rhododendron simsii',
'tax_id' => '118357',
'version' => 'v1.0',
'eco_type' => null
),
(int) 75 => array(
'species' => 'rch',
'common_name' => 'Rosa chinensis',
'tax_id' => '74649',
'version' => 'v2.0',
'eco_type' => null
),
(int) 76 => array(
'species' => 'sbr',
'common_name' => 'Salix brachista',
'tax_id' => '2182728',
'version' => 'v1.0',
'eco_type' => null
),
(int) 77 => array(
'species' => 'sbo',
'common_name' => 'Salvia bowleyana',
'tax_id' => '424416',
'version' => 'v1.0',
'eco_type' => 'Dunn'
),
(int) 78 => array(
'species' => 'shi',
'common_name' => 'Sapria himalayana',
'tax_id' => '289637',
'version' => 'v1.0',
'eco_type' => null
),
(int) 79 => array(
'species' => 'spa',
'common_name' => 'Schrenkiella parvula',
'tax_id' => '98039',
'version' => 'v2.2',
'eco_type' => null
),
(int) 80 => array(
'species' => 'sed',
'common_name' => 'Sechium edule',
'tax_id' => '184140',
'version' => 'v1.0',
'eco_type' => null
),
(int) 81 => array(
'species' => 'smo',
'common_name' => 'Selaginella moellendorffii',
'tax_id' => '88036',
'version' => 'v1.0',
'eco_type' => null
),
(int) 82 => array(
'species' => 'sun',
'common_name' => 'Selenicereus undatus',
'tax_id' => '176265',
'version' => 'v1.0',
'eco_type' => null
),
(int) 83 => array(
'species' => 'sgi',
'common_name' => 'Sequoiadendron giganteum',
'tax_id' => '99814',
'version' => 'V2.0',
'eco_type' => null
),
(int) 84 => array(
'species' => 'sci',
'common_name' => 'Simmondsia chinensis',
'tax_id' => '3999',
'version' => 'sc1',
'eco_type' => null
),
(int) 85 => array(
'species' => 'sly',
'common_name' => 'Solanum lycopersicum',
'tax_id' => '4081',
'version' => 'ITAG4.0',
'eco_type' => null
),
(int) 86 => array(
'species' => 'spe',
'common_name' => 'Solanum pennellii',
'tax_id' => '28526',
'version' => 'V2.0',
'eco_type' => null
),
(int) 87 => array(
'species' => 'stu',
'common_name' => 'Solanum tuberosum',
'tax_id' => '4113',
'version' => 'JGI v4.03',
'eco_type' => null
),
(int) 88 => array(
'species' => 'sas',
'common_name' => 'Striga asiatica',
'tax_id' => '4170',
'version' => 'v2.02',
'eco_type' => null
),
(int) 89 => array(
'species' => 'tha',
'common_name' => 'Tarenaya hassleriana',
'tax_id' => '28532',
'version' => 'RefSeq v1',
'eco_type' => null
),
(int) 90 => array(
'species' => 'tca',
'common_name' => 'Theobroma cacao',
'tax_id' => '3641',
'version' => 'V2.1',
'eco_type' => 'Matina 1-6'
),
(int) 91 => array(
'species' => 'tpr',
'common_name' => 'Trifolium pratense',
'tax_id' => '57577',
'version' => 'V2.0',
'eco_type' => null
),
(int) 92 => array(
'species' => 'twi',
'common_name' => 'Tripterygium wilfordii',
'tax_id' => '458696',
'version' => 'ASM1340144v1',
'eco_type' => null
),
(int) 93 => array(
'species' => 'tar',
'common_name' => 'Trochodendron aralioides',
'tax_id' => '4407',
'version' => 'v1.0',
'eco_type' => null
),
(int) 94 => array(
'species' => 'ugi',
'common_name' => 'Utricularia gibba',
'tax_id' => '13748',
'version' => 'v1.1F',
'eco_type' => null
),
(int) 95 => array(
'species' => 'vma',
'common_name' => 'Vaccinium macrocarpon',
'tax_id' => '13750',
'version' => 'V1.0',
'eco_type' => 'Stevens'
),
(int) 96 => array(
'species' => 'vpl',
'common_name' => 'Vanilla planifolia',
'tax_id' => '51239',
'version' => 'Elo Vpla-A Principal v1.0',
'eco_type' => 'Daphna'
),
(int) 97 => array(
'species' => 'vmu',
'common_name' => 'Vigna mungo',
'tax_id' => '3915',
'version' => 'ASM1342719v1',
'eco_type' => null
),
(int) 98 => array(
'species' => 'vvi',
'common_name' => 'Vitis vinifera',
'tax_id' => '29760',
'version' => 'Genoscope.12x',
'eco_type' => null
),
(int) 99 => array(
'species' => 'zma',
'common_name' => 'Zea mays',
'tax_id' => '4577',
'version' => 'NAM v5.0',
'eco_type' => 'B73'
)
)
$species_2_common = array(
'acertr' => 'Acer truncatum',
'ach' => 'Actinidia chinensis',
'aar' => 'Aethionema arabicum',
'amhyb' => 'Amaranthus hybridus',
'atr' => 'Amborella trichopoda',
'aag' => 'Anthoceros agrestis',
'aox' => 'Aquilegia oxysepala',
'aly' => 'Arabidopsis lyrata',
'ath' => 'Arabidopsis thaliana',
'arhy' => 'Arachis hypogaea',
'ama' => 'Avicennia marina',
'bvu' => 'Beta vulgaris',
'bca' => 'Brassica carinata',
'bna' => 'Brassica napus',
'bol' => 'Brassica oleracea',
'bra' => 'Brassica rapa',
'camsi' => 'Camellia sinensis var. sinensis',
'cansat' => 'Cannabis sativa',
'cru' => 'Capsella rubella',
'can' => 'Capsicum annuum',
'chi' => 'Cardamine hirsuta',
'cpa' => 'Carica papaya',
'cfa' => 'Carpinus fangiana',
'cil' => 'Carya illinoinensis',
'cde' => 'Ceratophyllum demersum',
'cbr' => 'Chara braunii',
'cqu' => 'Chenopodium quinoa',
'cre' => 'Chlamydomonas reinhardtii',
'car' => 'Cicer arietinum L.',
'cla' => 'Citrullus lanatus',
'ccl' => 'Citrus clementina',
'ccan' => 'Coffea canephora',
'col' => 'Corchorus olitorius',
'cav' => 'Corylus avellana',
'cme' => 'Cucumis melo',
'csa' => 'Cucumis sativus L.',
'dca' => 'Daucus carota',
'din' => 'Davidia involucrata',
'dzi' => 'Durio zibethinus',
'eca' => 'Erigeron canadensis',
'egut' => 'Erythranthe guttata',
'egr' => 'Eucalyptus grandis',
'esa' => 'Eutrema salsugineum',
'fve' => 'Fragaria vesca',
'fan' => 'Fragaria x ananassa',
'gma' => 'Glycine max',
'ghi' => 'Gossypium hirsutum',
'gra' => 'Gossypium raimondii',
'han' => 'Helianthus annuus',
'hma' => 'Hydrangea macrophylla',
'lsa' => 'Lactuca sativa',
'lonja' => 'Lonicera japonica',
'lja' => 'Lotus japonicus',
'lal' => 'Lupinus albus',
'mbi' => 'Magnolia biondii',
'mdo' => 'Malus domestica',
'mes' => 'Manihot esculenta',
'mpo' => 'Marchantia polymorpha',
'mtr' => 'Medicago truncatula',
'mco' => 'Micromonas commoda',
'nnu' => 'Nelumbo nucifera',
'nta' => 'Nicotiana tabacum',
'oeu' => 'Olea europaea',
'osa' => 'Oryza sativa ssp. japonica',
'pso' => 'Papaver somniferum',
'pax' => 'Petunia axillaris',
'pvu' => 'Phaseolus vulgaris',
'ppa' => 'Physcomitrium patens',
'psa' => 'Pisum sativum',
'ptr' => 'Populus trichocarpa',
'pco' => 'Prasinoderma coloniale',
'ppe' => 'Prunus persica',
'pgr' => 'Punica granatum',
'qlo' => 'Quercus lobata',
'rsi' => 'Rhododendron simsii',
'rch' => 'Rosa chinensis',
'sbr' => 'Salix brachista',
'sbo' => 'Salvia bowleyana',
'shi' => 'Sapria himalayana',
'spa' => 'Schrenkiella parvula',
'sed' => 'Sechium edule',
'smo' => 'Selaginella moellendorffii',
'sun' => 'Selenicereus undatus',
'sgi' => 'Sequoiadendron giganteum',
'sci' => 'Simmondsia chinensis',
'sly' => 'Solanum lycopersicum',
'spe' => 'Solanum pennellii',
'stu' => 'Solanum tuberosum',
'sas' => 'Striga asiatica',
'tha' => 'Tarenaya hassleriana',
'tca' => 'Theobroma cacao',
'tpr' => 'Trifolium pratense',
'twi' => 'Tripterygium wilfordii',
'tar' => 'Trochodendron aralioides',
'ugi' => 'Utricularia gibba',
'vma' => 'Vaccinium macrocarpon',
'vpl' => 'Vanilla planifolia',
'vmu' => 'Vigna mungo',
'vvi' => 'Vitis vinifera',
'zma' => 'Zea mays'
)
$clades_with_species = array()
$matches = null
preg_match_all - [internal], line ??
PhylogenyUtilsComponent::getCladeSizePerSpecies() - APP/Controller/Component/PhylogenyUtilsComponent.php, line 469
InstanceController::instances_locate() - APP/Controller/InstanceController.php, line 104
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 193
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 163