Statistics on protein trees

The protein tree pipeline is described at the following page.

• Overview
• Gene tree coverage and Gene QC for each species
• Size of gene trees (split by their root taxon)
• Gene tree nodes, and the inference of speciation / duplication events

Overall Summary

Legend
Internal nodes (ancestral taxa)	Node types	Speciations	Duplications	Dubious nodes
Leaves (extant species)	Gene tree coverage	Genes in multi-species trees	Genes in single-species trees	Orphaned genes
	Gene QC	Validated genes	Short genes	Long genes	Split genes

Arthrobotrys oligospora ATCC 24927

Dactylellina haptotyla CBS 200.50

Drechslerella stenobrocha 248

Tuber magnatum

Tuber melanosporum Mel28

Tuber borchii

Oidiodendron maius Zn

Amorphotheca resinae ATCC 22711

Erysiphe pulchra

Erysiphe necator

Blumeria graminis f. sp. hordei DH14

Meliniomyces bicolor E

Hyaloscypha variabilis F

Glarea lozoyensis ATCC 20868

Marssonina brunnea f. sp. 'multigermtubi' MB_m1

Diplocarpon rosae

Sclerotinia borealis F-4128

Sclerotinia sclerotiorum 1980 UF-70 ASM14694v1

Botrytis cinerea B05.10

Phialocephala scopiformis

Phialocephala subalpina

Rhynchosporium agropyri

Rhynchosporium secalis

Rhynchosporium commune

Cadophora sp. DSE1049

Rutstroemia sp. NJR-2017a BBW

Rutstroemia sp. NJR-2017a WRK4

Rutstroemia sp. NJR-2017a BVV2

Pezoloma ericae

Verticillium dahliae VdLs.17

Verticillium longisporum vl2.denovo.v1

Colletotrichum graminicola M1.001

Colletotrichum fructicola Nara gc5

Colletotrichum orbiculare MAFF 240422

Colletotrichum higginsianum

Ceratocystis platani

Thielaviopsis punctulata

Scedosporium apiospermum

Lomentospora prolificans

Acremonium chrysogenum ATCC 11550

Ustilaginoidea virens Assembly_for_version_1_of_the_Villosiclava_virens_genome

Fusarium verticillioides 7600

Fusarium fujikuroi EF1

Fusarium pseudograminearum CS3096

Fusarium graminearum CS3005v1

Fusarium culmorum CS7071

Fusarium oxysporum f. sp. lycopersici 4287 FO2

[Nectria] haematococca mpVI 77-13-4

Neonectria ditissima

Trichoderma virens Gv29-8

Trichoderma asperellum CBS 433.97

Trichoderma parareesei

Trichoderma citrinoviride

Trichoderma gamsii

Trichoderma reesei QM6a

Trichoderma longibrachiatum ATCC 18648

Trichoderma guizhouense

Trichoderma atroviride IMI 206040

Trichoderma harzianum ASM98886v1

Escovopsis weberi

Beauveria brongniartii RCEF 3172

Cordyceps fumosorosea ARSEF 2679

Cordyceps militaris CM01

Cordyceps confragosa RCEF 1005

Cordyceps sp. RAO-2017

Beauveria bassiana ASM168263v1

Stachybotrys chlorohalonata IBT 40285

Stachybotrys chartarum IBT 40288

Ophiocordyceps camponoti-rufipedis

Ophiocordyceps australis OphauG2

Tolypocladium paradoxum

Tolypocladium capitatum

Tolypocladium ophioglossoides CBS 100239

Purpureocillium lilacinum ASM165320v1

Hirsutella minnesotensis 3608

Drechmeria coniospora

Metarhizium album ARSEF 1941

Metarhizium robertsii ARSEF 23

Metarhizium acridum CQMa 102

Metarhizium rileyi RCEF 4871

Metarhizium majus ARSEF 297

Moelleriella libera RCEF 2490

Pochonia chlamydosporia 170

Torrubiella hemipterigena

Claviceps purpurea 20.1

Hypoxylon sp. CI-4A

Daldinia sp. EC12

Pseudomassariella vexata

Microdochium bolleyi

Rosellinia necatrix

Pestalotiopsis fici W106-1

Eutypa lata UCREL1

Sporothrix brasiliensis 5110

Sporothrix insectorum RCEF 264

Sporothrix schenckii ATCC 58251

Grosmannia clavigera kw1407

Ophiostoma piceae UAMH 11346

Gaeumannomyces tritici R3-111a-1

Pyricularia oryzae 70-15

Magnaporthiopsis poae ATCC 64411

Neurospora tetrasperma FGSC 2509

Neurospora crassa OR74A

Sordaria macrospora k-hell

Chaetomium thermophilum var. thermophilum DSM 1495

Chaetomium globosum CBS 148.51

Thielavia terrestris NRRL 8126

Thermothelomyces thermophilus ATCC 42464

Madurella mycetomatis

Diaporthe ampelina

Diaporthe helianthi

Coniella lustricola

Valsa mali var. pyri

Coniochaeta ligniaria NRRL 30616

Phaeoacremonium minimum UCRPA7

Talaromyces islandicus

Talaromyces stipitatus ATCC 10500

Talaromyces atroroseus

Talaromyces cellulolyticus

Talaromyces marneffei ATCC 18224

Rasamsonia emersonii CBS 393.64

Penicillium camemberti FM 013

Penicillium brasilianum Pbras_Allpaths-LG

Penicillium antarcticum

Aspergillus fischeri NRRL 181

Aspergillus clavatus NRRL 1

Aspergillus terreus NIH2624

Aspergillus oryzae RIB40

Aspergillus niger ASM285v2

Aspergillus fumigatus

Aspergillus flavus NRRL3357

Aspergillus nidulans FGSC A4 ASM1142v1

Penicilliopsis zonata CBS 506.65

Elaphomyces granulatus

Byssochlamys spectabilis No. 5

Paracoccidioides lutzii Pb01

Paracoccidioides brasiliensis Pb18

Coccidioides posadasii str. Silveira

Coccidioides immitis H538.4

Trichophyton equinum CBS 127.97

Trichophyton soudanense CBS 452.61

Trichophyton benhamiae CBS 112371

Trichophyton violaceum

Trichophyton interdigitale MR816

Trichophyton mentagrophytes

Trichophyton tonsurans CBS 112818

Trichophyton verrucosum HKI 0517

Trichophyton rubrum CBS 118892

Microsporum canis CBS 113480

Nannizzia gypsea CBS 118893

Blastomyces silveriae

Emmonsia sp. CAC-2015a

Emmonsia crescens UAMH 3008

Blastomyces percursus

Blastomyces dermatitidis ER-3

Blastomyces gilchristii SLH14081

Polytolypa hystricis UAMH7299

Histoplasma capsulatum NAm1

Emergomyces pasteurianus Ep9510

Helicocarpus griseus UAMH5409

Ascosphaera apis ARSEF 7405

Uncinocarpus reesii 1704

Phialophora americana

Phialophora attae

Capronia epimyces CBS 606.96

Capronia coronata CBS 617.96

Fonsecaea monophora

Fonsecaea nubica

Fonsecaea erecta

Fonsecaea pedrosoi CBS 271.37

Fonsecaea multimorphosa CBS 102226

Cladophialophora psammophila CBS 110553

Cladophialophora carrionii

Cladophialophora bantiana CBS 173.52

Cladophialophora immunda

Cladophialophora yegresii CBS 114405

Exophiala sideris

Exophiala mesophila

Exophiala aquamarina CBS 119918

Exophiala dermatitidis NIH/UT8656

Exophiala xenobiotica

Exophiala spinifera

Exophiala oligosperma

Rhinocladiella mackenziei CBS 650.93

Cyphellophora europaea CBS 101466

Endocarpon pusillum Z07020

Phaeomoniella chlamydospora

Rachicladosporium antarcticum

Rachicladosporium sp. CCFEE 5018

Hortaea werneckii EXF-2000

Baudoinia panamericana UAMH 10762

Pseudocercospora musae

Pseudocercospora fijiensis CIRAD86

Zymoseptoria tritici IPO323

Zymoseptoria brevis

Cercospora beticola

Cercospora berteroae

Cercospora zeina

Ramularia collo-cygni

Pseudocercospora eumusae

Dothistroma septosporum NZE10

Sphaerulina musiva SO2202

Aureobasidium melanogenum CBS 110374

Aureobasidium subglaciale EXF-2481

Aureobasidium pullulans EXF-150

Aureobasidium namibiae CBS 147.97

Elsinoe australis

Diplodia corticola

Diplodia seriata UCDDS831v0.1

Macrophomina phaseolina MS6

Neofusicoccum parvum UCRNP2

Acidomyces richmondensis BFW

Coniosporium apollinis CBS 100218

Periconia macrospinosa

Paraphaeosphaeria sporulosa

Stagonospora sp. SRC1lsM3a

Ascochyta rabiei

Epicoccum nigrum

Pyrenophora tritici-repentis Pt-1C-BFP

Pyrenophora teres f. teres 0-1

Bipolaris victoriae FI3

Bipolaris maydis C5

Bipolaris zeicola 26-R-13

Bipolaris sorokiniana ND90Pr

Bipolaris oryzae ATCC 44560

Stemphylium lycopersici

Exserohilum turcica Et28A

Alternaria alternata

Leptosphaeria maculans JN3

Parastagonospora nodorum SN15

Pyrenochaeta sp. DS3sAY3a

Clohesyomyces aquaticus

Corynespora cassiicola Philippines

Xylona heveae TC161

Nadsonia fulvescens var. elongata DSM 6958

Kuraishia capsulata CBS 1993

Sugiyamaella lignohabitans

Wickerhamiella sorbophila

[Candida] auris ASM118947v1

Clavispora lusitaniae ATCC 42720

Metschnikowia bicuspidata var. bicuspidata NRRL YB-4993

Pichia kudriavzevii ASM76445v1

Pichia membranifaciens NRRL Y-2026

Ogataea polymorpha

Ogataea parapolymorpha DL-1

Brettanomyces bruxellensis AWRI1499

Komagataella phaffii GS115 GCA_000027005.1

Komagataella phaffii GS115 ASM174695v1

Wickerhamomyces ciferrii

Wickerhamomyces anomalus NRRL Y-366-8

Cyberlindnera fabianii ASM320585v1

Cyberlindnera jadinii

Hanseniaspora guilliermondii

Hanseniaspora valbyensis NRRL Y-1626

Hanseniaspora uvarum DSM 2768

Hanseniaspora opuntiae

Hanseniaspora osmophila

Candida albicans SC5314 Cand_albi_SC5314_V4

Candida tropicalis MYA-3404

Candida parapsilosis

Lodderomyces elongisporus NRRL YB-4239

Debaryomyces fabryi

Debaryomyces hansenii CBS767

Hyphopichia burtonii NRRL Y-1933

Millerozyma farinosa CBS 7064

Meyerozyma guilliermondii ATCC 6260

Spathaspora passalidarum NRRL Y-27907

Scheffersomyces stipitis CBS 6054

Babjeviella inositovora NRRL Y-12698

Suhomyces tanzawaensis NRRL Y-17324

Naumovozyma dairenensis CBS 421

Naumovozyma castellii CBS 4309

Eremothecium gossypii ATCC 10895

Eremothecium gossypii FDAG1

Eremothecium cymbalariae DBVPG#7215

Lachancea lanzarotensis

Lachancea dasiensis CBS 10888

Kazachstania naganishii CBS 8797

Kazachstania africana CBS 2517

Tetrapisispora blattae CBS 6284

Tetrapisispora phaffii CBS 4417

Zygosaccharomyces bailii CLIB 213

Zygosaccharomyces rouxii ASM2636v1

Zygosaccharomyces parabailii

Kluyveromyces lactis

Kluyveromyces marxianus DMKU3-1042

Kluyveromyces dobzhanskii CBS 2104

Saccharomyces eubayanus

Saccharomyces arboricola H-6

Saccharomyces cerevisiae S288C

Saccharomyces kudriavzevii IFO 1802

Saccharomyces sp. 'boulardii' ASM129837v2

Torulaspora delbrueckii

Pachysolen tannophilus NRRL Y-2460

Vanderwaltozyma polyspora DSM 70294

[Candida] glabrata ASM254v2

Saccharomycetaceae sp. 'Ashbya aceri'

Tortispora caseinolytica NRRL Y-17796

Ascoidea rubescens DSM 1968

Yarrowia lipolytica YALIA101

Lipomyces starkeyi NRRL Y-11557

Pneumocystis jirovecii RU7

Pneumocystis murina B123

Pneumocystis carinii B80

Schizosaccharomyces japonicus yFS275

Schizosaccharomyces cryophilus OY26

Schizosaccharomyces pombe 972h-

Schizosaccharomyces octosporus yFS286

Neolecta irregularis DAH-3

Protomyces lactucaedebilis

Saitoella complicata NRRL Y-17804 Scomplicata_3.0

Puccinia graminis f. sp. tritici 04KEN156/4

Puccinia graminis f. sp. tritici CRL 75-36-700-3

Puccinia sorghi

Puccinia striiformis

Puccinia triticina 1-1 BBBD Race 1

Puccinia coronata var. avenae f. sp. avenae

Melampsora larici-populina 98AG31

Microbotryum intermedium

Microbotryum lychnidis-dioicae p1A1 Lamole

Rhodotorula graminis WP1

Rhodotorula toruloides ATCC 204091

Leucosporidium creatinivorum

Mixia osmundae IAM 14324 Mosmundae_2.0

Calocera viscosa TUFC12733

Calocera cornea HHB12733

Dacryopinax primogenitus

Wallemia ichthyophaga EXF-994

Wallemia mellicola CBS 633.66

Cutaneotrichosporon oleaginosum

Trichosporon asahii var. asahii CBS 8904

Kwoniella dejecticola CBS 10117

Kwoniella bestiolae CBS 10118

Kwoniella pini CBS 10737

Cryptococcus amylolentus CBS 6039

Cryptococcus depauperatus CBS 7841

Cryptococcus gattii WM276

Cryptococcus neoformans var. neoformans JEC21

Tsuchiyaea wingfieldii CBS 7118

Tremella mesenterica DSM 1558

Kockovaella imperatae

Naematelia encephala

Piloderma croceum F 1598

Fibularhizoctonia sp. CBS 109695

Pisolithus microcarpus 441

Pisolithus tinctorius Marx 270

Scleroderma citrinum Foug A

Paxillus rubicundulus Ve08.2h10

Paxillus involutus ATCC 200175

Hydnomerulius pinastri MD-312

Coniophora puteana RWD-64-598 SS2

Serpula lacrymans var. lacrymans S7.3

Suillus luteus UH-Slu-Lm8-n1

Rhizopogon vesiculosus

Armillaria solidipes

Armillaria gallica

Armillaria ostoyae

Cylindrobasidium torrendii FP15055 ss-10

Laccaria bicolor S238N-H82

Laccaria amethystina LaAM-08-1

Termitomyces sp. J132

Hypsizygus marmoreus

Moniliophthora perniciosa FA553

Moniliophthora roreri MCA 2997

Amanita muscaria Koide BX008

Amanita thiersii Skay4041

Agaricus bisporus var. burnettii JB137-S8

Leucoagaricus sp. SymC.cos

Gymnopus luxurians FD-317 M1

Lentinula edodes

Hypholoma sublateritium FD-334 SS-4

Galerina marginata CBS 339.88

Pleurotus ostreatus PC15

Fistulina hepatica ATCC 64428

Coprinopsis cinerea okayama7#130

Hebeloma cylindrosporum h7

Schizophyllum commune H4-8

Plicaturopsis crispa FD-325 SS-3

Jaapia argillacea MUCL 33604

Neolentinus lepideus HHB14362 ss-1

Gloeophyllum trabeum ATCC 11539

Fomitiporia mediterranea MF3/22

Pyrrhoderma noxium

Schizopora paradoxa

Serendipita vermifera MAFF 305830

Serendipita indica DSM 11827

Sistotremastrum suecicum HHB10207 ss-3

Sistotremastrum niveocremeum HHB9708

Tulasnella calospora MUT 4182

Botryobasidium botryosum FD-172 SS1

Rhizoctonia solani AG-1 IA

Peniophora sp. CONT

Stereum hirsutum FP-91666 SS1

Heterobasidion irregulare TC 32-1

Fomitopsis pinicola FP-58527 SS1

Daedalea quercina L-15889

Phanerochaete carnosa HHB-10118-sp

Phlebiopsis gigantea 11061_1 CR5-6

Wolfiporia cocos MD-104 SS10

Laetiporus sulphureus 93-53

Trametes coccinea BRFM310

Trametes cinnabarina

Trametes pubescens

Trametes versicolor FP-101664 SS1

Dichomitus squalens LYAD-421 SS1

Ganoderma sinense ZZ0214-1

Grifola frondosa

Gelatoporia subvermispora B

Postia placenta Mad-698-R

Phlebia centrifuga

Fibroporia radiculosa

Exidia glandulosa HHB12029

Punctularia strigosozonata HHB-11173 SS5

Sphaerobolus stellatus SS14

Moesziomyces aphidis DSM 70725

Moesziomyces antarcticus T-34

Ustilago maydis 521

Ustilago hordei

Sporisorium reilianum SRZ2

Pseudozyma hubeiensis SY62

Kalmanozyma brasiliensis GHG001

Anthracocystis flocculosa PF-1

Testicularia cyperi

Malassezia globosa CBS 7966

Malassezia vespertilionis

Malassezia pachydermatis

Malassezia sympodialis ATCC 42132 ASM34930v2

Jaminaea rosea

Pseudomicrostroma glucosiphilum

Acaromyces ingoldii

Meira miltonrushii

Tilletia controversa

Tilletia indica

Tilletia caries

Tilletia walkeri

Tilletiopsis washingtonensis

Ceraceosorus guamensis

Tilletiaria anomala UBC 951

Violaceomyces palustris

Basidiobolus meristosporus CBS 931.73

Conidiobolus coronatus NRRL 28638

Paramicrosporidium saccamoebae

Rozella allomycis CSF55

Catenaria anguillulae PL171

Allomyces macrogynus ATCC 38327

Batrachochytrium dendrobatidis JEL423

Batrachochytrium salamandrivorans

Rhizoclosmatium globosum

Spizellomyces punctatus DAOM BR117

Piromyces sp. E2

Piromyces finnis

Anaeromyces robustus

Neocallimastix californiae

Gonapodya prolifera JEL478

Mortierella elongata AG-77

Mortierella verticillata NRRL 6337

Lobosporangium transversale

Absidia repens

Hesseltinella vesiculosa

Lichtheimia corymbifera JMRC:FSU:9682

Lichtheimia ramosa

Rhizopus delemar RA 99-880

Rhizopus microsporus Rmicro_CBS_344.29_Allpaths-LG

Mucor ambiguus

Mucor circinelloides f. circinelloides 1006PhL

Choanephora cucurbitarum

Syncephalastrum racemosum

Bifiguratus adelaidae

Rhizophagus clarus

Vavraia culicis subsp. floridensis