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

Phytomonas sp. isolate EM1 (GCA_000582765.1) (Phytomonas sp. EM1)

Phytomonas sp. isolate Hart1 (GCA_000982615.1) (Phytomonas sp. Hart1)

Leishmania infantum (GCA_900500625.1) (Leishmania infantum)

Leishmania donovani str. BPK282A1 (GCA_000227135.2) (Leishmania donovani)

Leishmania major (Leishmania major strain Friedlin)

Leishmania panamensis str. MHOM/PA/94/PSC-1 (GCA_000755165.1) (Leishmania panamensis)

Leptomonas pyrrhocoris str. H10 (GCA_001293395.1) (Leptomonas pyrrhocoris)

Leptomonas seymouri str. ATCC 30220 (GCA_001299535.1) (Leptomonas seymouri)

Angomonas deanei (GCA_000442575.2) (Angomonas deanei)

Strigomonas culicis (GCA_000442495.1) (Strigomonas culicis)

Trypanosoma conorhini (GCA_003719485.1) (Trypanosoma conorhini)

Trypanosoma theileri (GCA_002087225.1) (Trypanosoma theileri)

Trypanosoma brucei (Trypanosoma brucei)

Trypanosoma equiperdum (GCA_001457755.2) (Trypanosoma equiperdum)

Trypanosoma rangeli SC58 (GCA_000492115.1) (Trypanosoma rangeli SC58)

Trypanosoma cruzi marinkellei (GCA_000300495.1) (Trypanosoma cruzi marinkellei)

Perkinsela sp. CCAP 1560/4 (GCA_001235845.1) (Perkinsela sp. CCAP 1560/4)

Naegleria gruberi str. NEG-M (GCA_000004985.1) (Naegleria gruberi)

Spironucleus salmonicida (GCA_000497125.1) (Spironucleus salmonicida)

Giardia lamblia (Giardia lamblia ATCC 50803)

Kipferlia bialata (GCA_003568945.1) (Kipferlia bialata)

Tritrichomonas foetus str. K (GCA_001839685.1) (Tritrichomonas foetus)

Dictyostelium purpureum str. QSDP1 (GCA_000190715.1) (Dictyostelium purpureum)

Dictyostelium discoideum (Dictyostelium discoideum AX4)

Tieghemostelium lacteum str. TK (GCA_001606155.1) (Tieghemostelium lacteum)

Cavenderia fasciculata str. SH3 (GCA_000203815.1) (Cavenderia fasciculata)

Entamoeba invadens IP1 (GCA_000330505.1) (Entamoeba invadens IP1)

Entamoeba dispar SAW760 (GCA_000209125.2) (Entamoeba dispar SAW760)

Entamoeba nuttalli P19 (GCA_000257125.1) (Entamoeba nuttalli P19)

Entamoeba histolytica (Entamoeba histolytica HM-1:IMSS)

Planoprotostelium fungivorum str. Jena (GCA_003024175.1) (Planoprotostelium fungivorum)

Acanthamoeba castellanii str. Neff (GCA_000313135.1) (Acanthamoeba castellanii str. Neff)

Guillardia theta CCMP2712 (Guillardia theta CCMP2712)

Chroomonas mesostigmatica CCMP1168 (GCA_000286095.1) (Chroomonas mesostigmatica CCMP1168)

Cryptomonas paramecium str. CCAP977/2A (GCA_000194455.1) (Cryptomonas paramecium)

Blastocystis hominis str. Singapore isolate B (sub-type 7) (GCA_000151665.1) (Blastocystis hominis)

Hondaea fermentalgiana (GCA_002897355.1) (Hondaea fermentalgiana)

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444)

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531)

Pythium irregulare (Globisporangium irregulare DAOM BR486)

Pythium iwayamai (Globisporangium iwayamae DAOM BR242034)

Pythium ultimum (Globisporangium ultimum DAOM BR144)

Pythium vexans (Phytopythium vexans DAOM BR484)

Aphanomyces invadans str. NJM9701 (GCA_000520115.1) (Aphanomyces invadans Apha_inva_NJM9701_V1)

Aphanomyces astaci str. APO3 (GCA_000520075.1) (Aphanomyces astaci Apha_asta_APO3_V1)

Saprolegnia diclina VS20 (GCA_000281045.1) (Saprolegnia diclina VS20)

Saprolegnia parasitica CBS 223.65 (GCA_000151545.2) (Saprolegnia parasitica CBS 223.65)

Thraustotheca clavata str. ATCC 34112 (GCA_002081575.1) (Thraustotheca clavata)

Achlya hypogyna str. ATCC 48635 (GCA_002081595.1) (Achlya hypogyna)

Phytophthora sojae (Phytophthora sojae strain P6497)

Phytophthora nicotianae (GCA_001482985.1) (Phytophthora nicotianae ASM148298v1)

Phytophthora cactorum str. 10300 (GCA_003287315.1) (Phytophthora cactorum)

Phytophthora palmivora var. palmivora str. sbr112.9 (GCA_002911725.1) (Phytophthora palmivora var. palmivora)

Phytophthora megakarya str. zdho120 (GCA_002215365.1) (Phytophthora megakarya)

Phytophthora parasitica (Phytophthora parasitica P1569)

Phytophthora kernoviae (Phytophthora kernoviae 00238/432)

Phytophthora ramorum (Phytophthora ramorum)

Phytophthora infestans (Phytophthora infestans T30-4)

Phytophthora lateralis (Phytophthora lateralis MPF4)

Peronospora effusa (GCA_003704535.1) (Peronospora effusa Peff_R14)

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis Emoy2)

Plasmopara halstedii (GCA_900000015.1) (Plasmopara halstedii)

Nothophytophthora sp. Chile5 (GCA_001712635.2) (Nothophytophthora sp. Chile5)

Albugo laibachii (Albugo laibachii Nc14)

Pseudo-nitzschia multistriata (Pseudo-nitzschia multistriata)

Fragilariopsis cylindrus CCMP1102 (GCA_001750085.1) (Fragilariopsis cylindrus CCMP1102)

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1)

Thalassiosira oceanica str. CCMP1005 (GCA_000296195.2) (Thalassiosira oceanica)

Thalassiosira pseudonana (Thalassiosira pseudonana CCMP1335)

Aureococcus anophagefferens (GCA_000186865.1) (Aureococcus anophagefferens)

Ectocarpus siliculosus str. Ec 32 (CCAP 1310/04) (GCA_000310025.1) (Ectocarpus siliculosus)

Nannochloropsis gaditana CCMP526 (GCA_000240725.1) (Nannochloropsis gaditana CCMP526)

Reticulomyxa filosa (GCA_000512085.1) (Reticulomyxa filosa)

Bigelowiella natans (Bigelowiella natans CCMP2755)

Plasmodiophora brassicae (GCA_001049375.1) (Plasmodiophora brassicae)

Oxytricha trifallax str. JRB310 (GCA_000711775.1) (Oxytricha trifallax Oxytricha_MIC_v2.0)

Stylonychia lemnae str. 130c (GCA_000751175.1) (Stylonychia lemnae)

Ichthyophthirius multifiliis str. G5 (GCA_000220395.1) (Ichthyophthirius multifiliis)

Tetrahymena thermophila (Tetrahymena thermophila SB210)

Pseudocohnilembus persalinus (GCA_001447515.1) (Pseudocohnilembus persalinus)

Paramecium tetraurelia (Paramecium tetraurelia)

Stentor coeruleus (GCA_001970955.1) (Stentor coeruleus)

Theileria orientalis strain Shintoku (GCA_000740895.1) (Theileria orientalis strain Shintoku)

Theileria equi strain WA (GCA_000342415.1) (Theileria equi strain WA)

Theileria parva str. Muguga (GCA_000165365.1) (Theileria parva)

Babesia bovis str. T2Bo (GCA_000165395.1) (Babesia bovis)

Babesia bigemina str. Bond (GCA_000981445.1) (Babesia bigemina)

Babesia ovata str. Miyake (GCA_002897235.1) (Babesia ovata)

Babesia sp. Xinjiang (GCA_002095265.1) (Babesia sp. Xinjiang)

Plasmodium gallinaceum (GCA_900005855.1) (Plasmodium gallinaceum)

Plasmodium relictum (GCA_900005765.1) (Plasmodium relictum)

Plasmodium vinckei petteri str. CR (GCA_000524515.1) (Plasmodium vinckei petteri)

Plasmodium chabaudi (Plasmodium chabaudi chabaudi strain AS)

Plasmodium yoelii yoelii str. 17XNL (GCA_000003085.2) (Plasmodium yoelii yoelii)

Plasmodium berghei (Plasmodium berghei ANKA)

Plasmodium sp. gorilla clade G2 (GCA_900097015.1) (Plasmodium sp. gorilla clade G2)

Plasmodium reichenowi (GCA_001601855.1) (Plasmodium reichenowi ASM160185v1)

Plasmodium falciparum 3D7 (Plasmodium falciparum 3D7)

Plasmodium gaboni (GCA_001602025.1) (Plasmodium gaboni)

Plasmodium sp. DRC-Itaito (GCA_900240055.1) (Plasmodium sp. DRC-Itaito PGABG02)

Plasmodium ovale curtisi (GCA_900088565.1) (Plasmodium ovale curtisi Poc2)

Plasmodium fragile str. multiple (GCA_000956335.1) (Plasmodium fragile)

Plasmodium knowlesi (Plasmodium knowlesi strain H)

Plasmodium gonderi (GCA_002157705.1) (Plasmodium gonderi)

Plasmodium cynomolgi strain B (GCA_000321355.1) (Plasmodium cynomolgi strain B)

Plasmodium malariae (GCA_900088575.1) (Plasmodium malariae Pmal)

Plasmodium inui San Antonio 1 (GCA_000524495.1) (Plasmodium inui San Antonio 1)

Plasmodium vivax (Plasmodium vivax strain Salvador I)

Plasmodium coatneyi (GCA_001680005.1) (Plasmodium coatneyi)

Eimeria acervulina (GCA_000499425.1) (Eimeria acervulina)

Eimeria mitis (GCA_000499745.1) (Eimeria mitis)

Eimeria praecox (GCA_000499445.1) (Eimeria praecox)

Eimeria tenella str. Houghton (GCA_000499545.1) (Eimeria tenella)

Eimeria brunetti (GCA_000499725.1) (Eimeria brunetti)

Eimeria maxima str. Weybridge (GCA_000499605.1) (Eimeria maxima)

Cyclospora cayetanensis str. CHN_HEN01 (GCA_000769155.2) (Cyclospora cayetanensis)

Toxoplasma gondii ME49 (Toxoplasma gondii ME49)

Toxoplasma gondii VEG (GCA_000150015.2) (Toxoplasma gondii VEG)

Cystoisospora suis str. Wien I (GCA_002600585.1) (Cystoisospora suis)

Besnoitia besnoiti str. Bb-Ger1 (GCA_002563875.1) (Besnoitia besnoiti)

Hammondia hammondi str. H.H.34 (GCA_000258005.2) (Hammondia hammondi)

Cryptosporidium ubiquitum (GCA_001865345.1) (Cryptosporidium ubiquitum)

Cryptosporidium muris RN66 (GCA_000006515.1) (Cryptosporidium muris RN66)

Cryptosporidium andersoni (GCA_001865355.1) (Cryptosporidium andersoni)

Cryptosporidium meleagridis str. UKMEL1 (GCA_001593445.1) (Cryptosporidium meleagridis)

Cryptosporidium parvum Iowa II (GCA_000165345.1) (Cryptosporidium parvum Iowa II)

Gregarina niphandrodes (GCA_000223845.4) (Gregarina niphandrodes)

Perkinsus marinus ATCC 50983 str. PmCV4CB5 2B3 D4 (GCA_000006405.1) (Perkinsus marinus ATCC 50983)

Symbiodinium microadriaticum str. CCMP2467 (GCA_001939145.1) (Symbiodinium microadriaticum)

Monosiga brevicollis MX1 (GCA_000002865.1) (Monosiga brevicollis MX1)

Salpingoeca rosetta str. ATCC 50818 (GCA_000188695.1) (Salpingoeca rosetta)

Fonticula alba str. ATCC 38817 (GCA_000388065.2) (Fonticula alba)

Capsaspora owczarzaki ATCC 30864 (GCA_000151315.2) (Capsaspora owczarzaki ATCC 30864)

Sphaeroforma arctica JP610 (GCA_001186125.1) (Sphaeroforma arctica JP610)

Thecamonas trahens ATCC 50062 (GCA_000142905.1) (Thecamonas trahens ATCC 50062)

Emiliania huxleyi (Emiliania huxleyi CCMP1516)