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

Vigna angularis strain Jingnong 6

Vigna radiata var. radiata strain VC1973A

Vigna unguiculata cultivar IT97K-499-35

Glycine max strain Williams 82

Glycine soja

Cajanus cajan

Lablab purpureus

Phaseolus vulgaris strain G19833

Sphenostylis stenocarpa

Pisum sativum CAAS_Psat_ZW6_1.0

Pisum sativum JIC_Psat_v1.3

Pisum sativum cultivar Cameor

Lathyrus sativus

Vicia faba

Medicago truncatula

Trifolium pratense strain Milvus B

Arachis hypogaea

Lupinus angustifolius strain Tanjil

Prunus avium strain Satonishiki

Prunus dulcis strain Texas

Prunus persica strain Lovell

Malus domestica strain Golden Delicious

Rosa chinensis

Cannabis sativa

Ficus carica cultivar Dottato

Quercus lobata

Quercus suber isolate HL8

Corylus avellana cultivar Tombul

Juglans regia cultivar Chandler

Cucumis melo

Cucumis sativus strain 9930

Citrullus lanatus strain 97103

Manihot esculenta

Populus trichocarpa

Arabidopsis halleri subsp. gemmifera strain W302

Arabidopsis lyrata subsp. lyrata strain MN47

Arabidopsis thaliana strain Columbia

Camelina sativa strain dh55 (component G1)

Camelina sativa strain dh55 (component G2)

Camelina sativa strain dh55 (component G3)

Brassica juncea cultivar Sichuan Huangzi

Brassica napus strain Darmor-bzh

Brassica oleracea var. oleracea strain TO1000

Brassica rapa subsp. trilocularis cultivar R-o-18

Arabis alpina

Eutrema salsugineum

Corchorus capsularis strain CVL-1

Gossypium raimondii isolate GPD5lz

Theobroma cacao reference (Matina) cultivar

Citrus x clementina strain Clemenules

Pistacia vera strain Batoury

Corymbia citriodora subsp. variegata genotype CCV2-018

Eucalyptus grandis strain BRASUZ1

Vitis vinifera

Solanum lycopersicum cultivar Heinz 1706

Solanum tuberosum cultivar DM 1-3 516 R44

Capsicum annuum strain Criollo de Morelos 334

Nicotiana attenuata strain UT

Ipomoea triloba strain NCNSP0323

Fraxinus excelsior reference strain

Olea europaea subsp. europaea variety Farga

Sesamum indicum strain Zhongzhi No. 13

Coffea canephora strain DH200-94

Cynara cardunculus var. scolymus isolate 2C

Helianthus annuus cultivar XRQ/B

Lactuca sativa

Daucus carota subsp. sativus strain DH1

Actinidia chinensis var. chinensis strain Red5

Beta vulgaris subsp. vulgaris strain KWS2320 DH

Chenopodium quinoa strain PI614886

Kalanchoe fedtschenkoi

Triticum aestivum reference (Chinese spring) cultivar (component A)

Triticum dicoccoides strain Zavitan (Atlit2015) (component A)

Triticum spelta cultivar Spelta (component A)

Triticum timopheevii (component A)

Triticum turgidum subsp. durum strain svevo (component A)

Triticum urartu strain G1812 (PI428198)

Triticum aestivum reference (Chinese spring) cultivar (component B)

Triticum dicoccoides strain Zavitan (Atlit2015) (component B)

Triticum spelta cultivar Spelta (component B)

Triticum timopheevii (component B)

Triticum turgidum subsp. durum strain svevo (component B)

Aegilops tauschii subsp. strangulata strain AL8/78

Triticum aestivum reference (Chinese spring) cultivar (component D)

Triticum spelta cultivar Spelta (component D)

Triticum aestivum reference (Chinese spring) cultivar (component U)

Triticum turgidum subsp. durum strain svevo (component U)

Hordeum vulgare subsp. vulgare cultivar Morex

Secale cereale

Avena sativa cultivar sang (component A)

Avena sativa cultivar sang (component C)

Avena sativa cultivar sang (component D)

Avena sativa cultivar sang (component U)

Avena sativa cultivar OT3098 (component A)

Avena sativa cultivar OT3098 (component C)

Avena sativa cultivar OT3098 (component D)

Lolium perenne reference strain

Brachypodium distachyon strain Bd21

Oryza sativa Indica Group strain 93-11

Oryza sativa Japonica Group reference (Nipponbare) cultivar

Oryza barthii cultivar IRGC:105608

Oryza brachyantha cultivar IRGC:101232

Oryza glaberrima cultivar CG14

Oryza glumipatula

Oryza longistaminata

Oryza meridionalis cultivar OR44 (W2112)

Oryza nivara cultivar IRGC:100897

Oryza punctata cultivar IRGC:105690

Oryza rufipogon cultivar W1943

Leersia perrieri cultivar IRGC:105164

Saccharum spontaneum strain AP85-441 (component A)

Saccharum spontaneum strain AP85-441 (component B)

Saccharum spontaneum strain AP85-441 (component C)

Saccharum spontaneum strain AP85-441 (component D)

Sorghum bicolor strain BTx623

Zea mays strain B73

Setaria italica strain Yugu1

Setaria viridis strain A10

Digitaria exilis strain digitaria_exilis

Echinochloa crus-galli reference strain

Panicum hallii var. hallii reference (HAL2) ecotype

Eragrostis curvula strain Tanganyika

Eragrostis tef cultivar Dabbi

Ananas comosus strain F153

Musa acuminata subsp. malaccensis cultivar Doubled-haploid Pahang (DH-Pahang)

Asparagus officinalis strain DH00/086

Dioscorea cayenensis subsp. rotundata

Papaver somniferum strain High Noscapine 1 (HN1)

Amborella trichopoda

Nymphaea colorata isolate Beijing-Zhang1983

Selaginella moellendorffii

Marchantia polymorpha

Physcomitrium patens strain Gransden 2004

Chara braunii strain S276

Chlamydomonas reinhardtii strain CC-503 cw92 mt+

Ostreococcus lucimarinus CCE9901

Caenorhabditis elegans strain N2

Drosophila melanogaster

Ciona savignyi

Homo sapiens

Saccharomyces cerevisiae S288C

Cyanidioschyzon merolae strain 10D

Galdieria sulphuraria strain 074W

Chondrus crispus strain Stackhouse