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

Physcomitrium patens (Physcomitrium patens strain Gransden 2004)

Marchantia polymorpha (Marchantia polymorpha strain Tak-1)

Selaginella moellendorffii (Selaginella moellendorffii)

Prunus persica (Prunus persica strain Lovell)

Prunus dulcis (Prunus dulcis strain Texas)

Prunus avium (Prunus avium strain Satonishiki)

Malus domestica Golden (Malus domestica strain Golden Delicious)

Rosa chinensis (Rosa chinensis)

Cannabis sativa female (Cannabis sativa)

Ficus carica (Ficus carica cultivar Dottato)

Corylus avellana (Corylus avellana cultivar Tombul)

Juglans regia (Juglans regia cultivar Chandler)

Quercus lobata (Quercus lobata)

Quercus suber (Quercus suber reference strain)

Vigna radiata (Vigna radiata var. radiata strain VC1973A)

Vigna angularis (Vigna angularis strain Jingnong 6)

Vigna unguiculata (Vigna unguiculata strain IT97K-499-35)

Phaseolus vulgaris (Phaseolus vulgaris strain G19833)

Glycine soja (Wild soybean) (Glycine soja)

Glycine max (Glycine max strain Williams 82)

Cajanus cajan (pigeon pea) - GCA_000340665.1 (Cajanus cajan)

Trifolium pratense (Trifolium pratense strain Milvus B)

Medicago truncatula (Medicago truncatula strain A17)

Pisum sativum (Pisum sativum cultivar Cameor)

Lupinus angustifolius (Lupinus angustifolius strain Tanjil)

Cucumis melo (Cucumis melo)

Cucumis sativus (Cucumis sativus strain 9930)

Citrullus lanatus (Citrullus lanatus strain 97103)

Pistacia vera (Pistacia vera strain Batoury)

Citrus clementina (Citrus clementina strain Clemenules)

Theobroma cacao Matina 1-6 (Theobroma cacao reference (Matina) cultivar)

Corchorus capsularis (Corchorus capsularis strain CVL-1)

Gossypium raimondii (Gossypium raimondii)

Manihot esculenta (Manihot esculenta strain AM560-2)

Populus trichocarpa (Populus trichocarpa)

Eucalyptus grandis (Eucalyptus grandis strain BRASUZ1)

Corymbia citriodora (Corymbia citriodora subsp. variegata genotype CCV2-018)

Vitis vinifera (Vitis vinifera strain PN40024)

Brassica napus (Brassica napus strain Darmor-bzh)

Brassica oleracea (Brassica oleracea var. oleracea strain TO1000)

Brassica juncea (Brassica juncea cultivar Sichuan Huangzi)

Brassica rapa R-o-18 (Brassica rapa subsp. trilocularis cultivar R-o-18)

Eutrema salsugineum (Eutrema salsugineum)

Arabis alpina (Arabis alpina)

Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata strain MN47)

Arabidopsis halleri (Arabidopsis halleri subsp. gemmifera strain W302)

Arabidopsis thaliana (Arabidopsis thaliana strain Columbia)

Camelina sativa (component G1) (Camelina sativa strain dh55 (component G1))

Camelina sativa (component G2) (Camelina sativa strain dh55 (component G2))

Kalanchoe fedtschenkoi (Kalanchoe fedtschenkoi)

Solanum tuberosum (Solanum tuberosum cultivar DM 1-3 516 R44)

Solanum lycopersicum (Solanum lycopersicum strain Heinz 1706)

Capsicum annuum (Capsicum annuum strain Criollo de Morelos 334)

Nicotiana attenuata (Nicotiana attenuata strain UT)

Ipomoea triloba (Ipomoea triloba strain NCNSP0323)

Olea europaea (Olea europaea subsp. europaea variety Farga)

Fraxinus excelsior (Fraxinus excelsior reference strain)

Sesamum indicum (Sesamum indicum strain Zhongzhi No. 13)

Coffea canephora (Coffea canephora strain DH200-94)

Cynara cardunculus (Cynara cardunculus var. scolymus)

Lactuca sativa (Lactuca sativa cultivar Salinas)

Helianthus annuus (Helianthus annuus cultivar XRQ/B)

Daucus carota (Daucus carota subsp. sativus strain DH1)

Actinidia chinensis (Actinidia chinensis var. chinensis strain Red5)

Beta vulgaris (Beta vulgaris subsp. vulgaris strain KWS2320 DH)

Chenopodium quinoa (Chenopodium quinoa strain PI614886)

Papaver somniferum (Papaver somniferum strain High Noscapine 1 (HN1))

Avena sativa OT3098 (Avena sativa strain OT3098)

Avena sativa Sang (Avena sativa strain sang)

Lolium perenne (Lolium perenne reference strain)

Aegilops tauschii (Aegilops tauschii subsp. strangulata strain AL8/78)

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

Triticum turgidum (component B) (Triticum turgidum subsp. durum strain svevo (component B))

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

Triticum dicoccoides (component B) (Triticum dicoccoides strain Zavitan (Atlit2015) (component B))

Secale cereale (Secale cereale)

Hordeum vulgare (Hordeum vulgare subsp. vulgare cultivar Morex)

Brachypodium distachyon (Brachypodium distachyon strain Bd21)

Oryza rufipogon (Oryza rufipogon cultivar W1943)

Oryza sativa Japonica Group (Oryza sativa Japonica Group reference (Nipponbare) cultivar)

Oryza sativa Indica Group (Oryza sativa Indica Group strain 93-11)

Oryza nivara (Oryza nivara cultivar IRGC:100897)

Oryza barthii (Oryza barthii cultivar IRGC:105608)

Oryza glaberrima (Oryza glaberrima cultivar CG14)

Oryza glumipatula (Oryza glumipatula)

Oryza longistaminata (Oryza longistaminata)

Oryza meridionalis (Oryza meridionalis cultivar OR44 (W2112))

Oryza punctata (Oryza punctata cultivar IRGC:105690)

Leersia perrieri (Leersia perrieri cultivar IRGC:105164)

Oryza brachyantha (Oryza brachyantha cultivar IRGC:101232)

Setaria italica (Setaria italica strain Yugu1)

Setaria viridis (Setaria viridis strain A10)

Panicum hallii HAL2 (Panicum hallii var. hallii reference (HAL2) ecotype)

Echinochloa crus-galli (Echinochloa crus-galli reference strain)

Digitaria exilis (Digitaria exilis strain digitaria_exilis)

Saccharum spontaneum (component B) (Saccharum spontaneum strain AP85-441 (component B))

Saccharum spontaneum (component A) (Saccharum spontaneum strain AP85-441 (component A))

Saccharum spontaneum (component C) (Saccharum spontaneum strain AP85-441 (component C))

Sorghum bicolor (Sorghum bicolor strain BTx623)

Zea mays (Zea mays strain B73)

Eragrostis curvula (Eragrostis curvula strain Tanganyika)

Eragrostis tef (Eragrostis tef cultivar Dabbi)

Ananas comosus (Ananas comosus strain F153)

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

Asparagus officinalis (Asparagus officinalis strain DH00/086)

Dioscorea rotundata (Dioscorea cayenensis subsp. rotundata)

Amborella trichopoda (Amborella trichopoda)

Nymphaea colorata (Nymphaea colorata strain Beijing-Zhang1983)

Triticum turgidum (component U) (Triticum turgidum subsp. durum strain svevo (component U))

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

Chara braunii (Chara braunii strain S276)

Chlamydomonas reinhardtii (Chlamydomonas reinhardtii strain CC-503 cw92 mt+)

Ostreococcus lucimarinus (Ostreococcus lucimarinus CCE9901)

C.savignyi (Ciona savignyi)

Human (Homo sapiens)

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

Caenorhabditis elegans (Nematode, N2) (Caenorhabditis elegans strain N2)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)

Chondrus crispus (Chondrus crispus strain Stackhouse)

Galdieria sulphuraria (Galdieria sulphuraria strain 074W)

Cyanidioschyzon merolae (Cyanidioschyzon merolae strain 10D)