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

Fusarium culmorum CS7071 strain UK99

Fusarium graminearum PH-1

Fusarium pseudograminearum CS3096

Fusarium fujikuroi strain IMI 58289

Fusarium verticillioides 7600

Fusarium oxysporum f. sp. lycopersici 4287

Fusarium vanettenii 77-13-4 strain MPVI 77-13-4

Neonectria ditissima

Tolypocladium capitatum

Tolypocladium ophioglossoides CBS 100239

Tolypocladium paradoxum

Ophiocordyceps australis OphauG2

Ophiocordyceps camponoti-rufipedis

Drechmeria coniospora

Hirsutella minnesotensis 3608

Purpureocillium lilacinum ASM165320v1

Metarhizium acridum CQMa 102

Metarhizium rileyi NOR_1.0

Claviceps purpurea 20.1

Moelleriella libera RCEF 2490

Pochonia chlamydosporia 170

Ustilaginoidea virens Assembly_for_version_1_of_the_Villosiclava_virens_genome

[Torrubiella] hemipterigena

Trichoderma asperellum CBS 433.97

Trichoderma atroviride IMI 206040

Trichoderma reesei QM6a

Trichoderma virens Gv29-8

Escovopsis weberi

Beauveria bassiana strain ARSEF 8028

Niveomyces insectorum RCEF 264

Stachybotrys chartarum IBT 40288

Stachybotrys chlorohalonatus IBT 40285

Hapsidospora chrysogenum ATCC 11550

Verticillium dahliae JR2

Verticillium dahliae VdLs.17

Verticillium longisporum vl2.denovo.v1

Colletotrichum fructicola Nara gc5

Colletotrichum graminicola M1.001

Colletotrichum higginsianum strain IMI 349063

Colletotrichum orbiculare MAFF 240422

Ceratocystis platani

Thielaviopsis punctulata

Lomentospora prolificans

Scedosporium apiospermum

Neurospora crassa OR74A

Sordaria macrospora k-hell

Chaetomium globosum CBS 148.51

Madurella mycetomatis

Sporothrix brasiliensis 5110

Sporothrix schenckii ATCC 58251

Grosmannia clavigera kw1407

Ophiostoma piceae UAMH 11346

Gaeumannomyces tritici R3-111a-1

Magnaporthiopsis poae ATCC 64411

Pyricularia oryzae strain BR32

Coniella lustricola

Cytospora mali ASM81338v1

Diaporthe ampelina

Coniochaeta ligniaria NRRL 30616

Phaeoacremonium minimum UCRPA7

Daldinia sp. EC12

Hypoxylon sp. CI-4A

Eutypa lata UCREL1

Rosellinia necatrix

Pestalotiopsis fici W106-1

Pseudomassariella vexata

Botrytis cinerea B05.10

Sclerotinia sclerotiorum 1980 UF-70

Cadophora sp. DSE1049

Rhynchosporium agropyri

Diplocarpon rosae

Drepanopeziza brunnea f. sp. 'multigermtubi' MB_m1

Mollisia scopiformis

Phialocephala subalpina

Amorphotheca resinae ATCC 22711

Glarea lozoyensis ATCC 20868

Hyaloscypha hepaticicola

Rutstroemia sp. NJR-2017a BBW

Erysiphe necator

Erysiphe pulchra

Blumeria hordei DH14 strain f. sp. hordei DH14

Oidiodendron maius Zn

Aspergillus fumigatus A1163

Aspergillus fumigatus Af293

Aspergillus clavatus NRRL 1

Aspergillus fischeri NRRL 181

Aspergillus flavus NRRL3357

Aspergillus niger ASM285v2

Aspergillus oryzae RIB40 strain RIB 40

Aspergillus terreus NIH2624

Aspergillus nidulans FGSC A4

Penicilliopsis zonata CBS 506.65

Penicillium antarcticum

Talaromyces atroroseus

Talaromyces islandicus

Talaromyces stipitatus ATCC 10500

Rasamsonia emersonii CBS 393.64

Elaphomyces granulatus

Paecilomyces variotii No. 5

Blastomyces dermatitidis ER-3

Helicocarpus griseus UAMH5409

Histoplasma ohiense (nom. inval.) strain G217B

Paracoccidioides brasiliensis Pb18

[Emmonsia] crescens ASM100828v1

Coccidioides immitis H538.4

Coccidioides posadasii str. Silveira

Uncinocarpus reesii 1704

Microsporum canis CBS 113480

Nannizzia gypsea CBS 118893

Trichophyton equinum CBS 127.97

Ascosphaera apis ARSEF 7405

Polytolypa hystricis UAMH7299

Capronia epimyces CBS 606.96

Cladophialophora carrionii

Exophiala aquamarina CBS 119918

Fonsecaea erecta

Phialophora americana

Rhinocladiella mackenziei CBS 650.93

Cyphellophora europaea CBS 101466

Endocarpon pusillum Z07020

Phaeomoniella chlamydospora

Bipolaris maydis C5

Bipolaris oryzae ATCC 44560

Pyrenophora teres f. teres 0-1

Pyrenophora tritici-repentis Pt-1C-BFP

Alternaria alternata Altal1

Exserohilum turcica Et28A

Stemphylium lycopersici ASM119154v1

Ascochyta rabiei

Epicoccum nigrum

Parastagonospora nodorum SN15

Phaeosphaeriaceae sp. SRC1lsM3a

Plenodomus lingam JN3

Pyrenochaeta sp. DS3sAY3a

Paraphaeosphaeria sporulosa

Periconia macrospinosa

Clohesyomyces aquaticus

Corynespora cassiicola Philippines

Pseudocercospora fijiensis CIRAD86

Pseudocercospora musae

Zymoseptoria brevis

Zymoseptoria tritici IPO323

Cercospora berteroae

Dothistroma septosporum NZE10

Ramularia collo-cygni

Sphaerulina musiva SO2202

Acidomyces richmondensis BFW

Baudoinia panamericana UAMH 10762

Hortaea werneckii EXF-2000

Cryoendolithus antarcticus

Rachicladosporium sp. CCFEE 5018

Aureobasidium melanogenum CBS 110374

Elsinoe australis ASM301379v1

Macrophomina phaseolina MS6

Neofusicoccum parvum UCRNP2

Coniosporium apollinis CBS 100218

Xylona heveae TC161

Dactylellina haptotyla CBS 200.50

Drechslerella stenobrocha 248

Orbilia oligospora ATCC 24927

Tuber borchii

Tuber magnatum

Tuber melanosporum Mel28

Candida albicans SC5314

Candida parapsilosis CDC317

Candida tropicalis MYA-3404

Lodderomyces elongisporus NRRL YB-4239

Debaryomyces hansenii CBS767

Hyphopichia burtonii NRRL Y-1933

Meyerozyma guilliermondii ATCC 6260

Millerozyma farinosa CBS 7064

Scheffersomyces stipitis CBS 6054

Spathaspora passalidarum NRRL Y-27907

Suhomyces tanzawaensis NRRL Y-17324

Candidozyma auris strain B8441

Candidozyma duobushaemuli strain B09383

Candidozyma haemuli strain B11899

Candidozyma pseudohaemuli strain B12108

Clavispora lusitaniae ATCC 42720

Metschnikowia bicuspidata var. bicuspidata NRRL YB-4993

Babjeviella inositovora NRRL Y-12698

Komagataella phaffii GS115

Komagataella phaffii GS115 ASM174695v1

Ogataea parapolymorpha DL-1

Ogataea polymorpha

Pichia kudriavzevii ASM76445v1

Pichia membranifaciens NRRL Y-2026

Brettanomyces bruxellensis AWRI1499

Kuraishia capsulata CBS 1993

Pachysolen tannophilus NRRL Y-2460

Eremothecium cymbalariae DBVPG#7215

Eremothecium gossypii FDAG1

Lachancea dasiensis

Lachancea lanzarotensis

Naumovozyma castellii

Naumovozyma dairenensis CBS 421

Zygosaccharomyces parabailii

Zygosaccharomyces rouxii ASM2636v1

Henningerozyma blattae CBS 6284

Huiozyma naganishii CBS 8797

Kazachstania africana CBS 2517

Nakaseomyces glabratus CBS 138

Saccharomyces cerevisiae S288C

Tetrapisispora phaffii CBS 4417

Torulaspora delbrueckii

Vanderwaltozyma polyspora DSM 70294

Cyberlindnera fabianii ASM320585v1

Cyberlindnera jadinii

Wickerhamomyces anomalus NRRL Y-366-8

Wickerhamomyces ciferrii

Ascoidea rubescens DSM 1968

Hanseniaspora guilliermondii

Nadsonia fulvescens var. elongata DSM 6958

Yarrowia lipolytica CLIB122

Sugiyamaella lignohabitans

Wickerhamiella sorbophila

Lipomyces starkeyi NRRL Y-11557

Tortispora caseinolytica NRRL Y-17796

Schizosaccharomyces cryophilus OY26

Schizosaccharomyces japonicus yFS275

Schizosaccharomyces octosporus yFS286

Schizosaccharomyces pombe 972h-

Pneumocystis carinii B80

Pneumocystis jirovecii RU7

Pneumocystis murina B123

Neolecta irregularis DAH-3

Protomyces lactucae-debilis

Armillaria gallica

Armillaria ostoyae

Armillaria solidipes

Cylindrobasidium torrendii FP15055 ss-10

Collybiopsis luxurians FD-317 M1

Lentinula edodes

Moniliophthora roreri MCA 2997

Agaricus bisporus var. burnettii JB137-S8

Leucoagaricus sp. SymC.cos

Galerina marginata CBS 339.88

Hypholoma sublateritium FD-334 SS-4

Coprinopsis cinerea okayama7#130

Hebeloma cylindrosporum

Laccaria amethystina LaAM-08-1

Amanita muscaria Koide BX008

Amanita thiersii Skay4041

Fistulina hepatica ATCC 64428

Schizophyllum commune H4-8

Hypsizygus marmoreus

Termitomyces sp. J132

Pleurotus ostreatus PC15

Pisolithus microcarpus 441

Pisolithus tinctorius Marx 270

Scleroderma citrinum Foug A

Coniophora puteana RWD-64-598 SS2

Serpula lacrymans var. lacrymans S7.3

Rhizopogon vesiculosus

Suillus luteus UH-Slu-Lm8-n1

Hydnomerulius pinastri MD-312

Paxillus involutus ATCC 200175

Athelia psychrophila

Piloderma croceum F 1598

Jaapia argillacea MUCL 33604

Plicaturopsis crispa FD-325 SS-3

Trametes cinnabarina

Trametes coccinea BRFM310

Dichomitus squalens LYAD-421 SS1

Ganoderma sinense ZZ0214-1

Daedalea quercina L-15889

Fomitopsis schrenkii

Phanerochaete chrysosporium RP-78

Phlebiopsis gigantea 11061_1 CR5-6

Fibroporia radiculosa

Gelatoporia subvermispora B

Grifola frondosa

Hermanssonia centrifuga ASM191385v2

Laetiporus sulphureus 93-53

Postia placenta Mad-698-R

Wolfiporia cocos MD-104 SS10

Botryobasidium botryosum FD-172 SS1

Rhizoctonia solani AG-1 IA

Tulasnella calospora MUT 4182

Heterobasidion irregulare TC 32-1

Peniophora sp. CONT

Stereum hirsutum FP-91666 SS1

Fomitiporia mediterranea MF3/22

Schizopora paradoxa

Gloeophyllum trabeum ATCC 11539

Neolentinus lepideus HHB14362 ss-1

Serendipita indica DSM 11827

Serendipita vermifera MAFF 305830

Sistotremastrum niveocremeum HHB9708

Sistotremastrum suecicum HHB10207 ss-3

Exidia glandulosa HHB12029

Punctularia strigosozonata HHB-11173 SS5

Sphaerobolus stellatus SS14

Cryptococcus deneoformans JEC21

Kwoniella bestiolae CBS 10118

Kockovaella imperatae

Naematelia encephala

Tremella mesenterica DSM 1558

Cutaneotrichosporon oleaginosum Triol1

Calocera cornea HHB12733

Calocera viscosa TUFC12733

Dacryopinax primogenitus

Pseudozyma flocculosa PF-1

Pseudozyma hubeiensis SY62

Kalmanozyma brasiliensis GHG001

Moesziomyces aphidis

Mycosarcoma maydis strain 521

Sporisorium reilianum SRZ2

Ustilago hordei

Testicularia cyperi

Acaromyces ingoldii

Meira miltonrushii

Jaminaea rosea

Pseudomicrostroma glucosiphilum

Ceraceosorus guamensis

Tilletiaria anomala UBC 951

Tilletiopsis washingtonensis

Puccinia coronata f. sp. avenae ASM287327v1

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

Puccinia sorghi

Puccinia striiformis f. sp. tritici PST-130

Puccinia triticina 1-1 BBBD Race 1

Melampsora larici-populina 98AG31

Rhodotorula graminis WP1

Rhodotorula toruloides ATCC 204091

Leucosporidium creatinivorum

Microbotryum lychnidis-dioicae p1A1 Lamole

Mixia osmundae IAM 14324 Mosmundae_2.0

Wallemia ichthyophaga EXF-994

Enterocytozoon bieneusi H348

Enterocytozoon hepatopenaei

Enterospora canceri

Vairimorpha apis BRL 01

Vittaforma corneae ATCC 50505

Hepatospora eriocheir ASM208787v1.0

Spraguea lophii 42_110

Amphiamblys sp. WSBS2006

Edhazardia aedis USNM 41457

Nematocida displodere

Ordospora colligata OC4

Pseudoloma neurophilia

Trachipleistophora hominis

Vavraia culicis subsp. floridensis

Anncaliia algerae PRA339

Rhizopus delemar RA 99-880

Rhizopus microsporus Rmicro_CBS_344.29_Allpaths-LG

Choanephora cucurbitarum

Mucor ambiguus

Absidia repens

Hesseltinella vesiculosa

Lichtheimia corymbifera JMRC:FSU:9682

Lichtheimia ramosa

Syncephalastrum racemosum

Bifiguratus adelaidae

Linnemannia elongata AG-77

Lobosporangium transversale

Podila verticillata NRRL 6337

Anaeromyces robustus

Neocallimastix californiae

Piromyces finnis

Batrachochytrium dendrobatidis JEL423

Rhizoclosmatium globosum

Spizellomyces punctatus DAOM BR117

Gonapodya prolifera JEL478

Paramicrosporidium saccamoebae

Rozella allomycis CSF55

Allomyces macrogynus ATCC 38327

Conidiobolus coronatus NRRL 28638