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

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 histolytica (Entamoeba histolytica HM-1:IMSS)

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

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

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

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)

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

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

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)

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

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

Angomonas deanei (GCA_000442575.2) (Angomonas deanei)

Strigomonas culicis (GCA_000442495.1) (Strigomonas culicis)

Trypanosoma brucei (Trypanosoma brucei)

Trypanosoma equiperdum (GCA_001457755.2) (Trypanosoma equiperdum)

Trypanosoma theileri (GCA_002087225.1) (Trypanosoma theileri)

Trypanosoma conorhini (GCA_003719485.1) (Trypanosoma conorhini)

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

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

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)

Hondaea fermentalgiana (GCA_002897355.1) (Hondaea fermentalgiana)

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

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444)

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531)

Pythium irregulare (Globisporangium irregulare DAOM BR486)

Pythium ultimum (Globisporangium ultimum DAOM BR144)

Pythium iwayamai (Globisporangium iwayamae DAOM BR242034)

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

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

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

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

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

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

Phytophthora ramorum (Phytophthora ramorum)

Phytophthora kernoviae (Phytophthora kernoviae 00238/432)

Phytophthora lateralis (Phytophthora lateralis MPF4)

Phytophthora parasitica (Phytophthora parasitica P1569)

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

Phytophthora sojae (Phytophthora sojae strain P6497)

Phytophthora infestans (Phytophthora infestans T30-4)

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

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

Plasmopara halstedii (GCA_900000015.1) (Plasmopara halstedii)

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis Emoy2)

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

Albugo laibachii (Albugo laibachii Nc14)

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

Pseudo-nitzschia multistriata (Pseudo-nitzschia multistriata)

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1)

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

Thalassiosira pseudonana (Thalassiosira pseudonana CCMP1335)

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

Aureococcus anophagefferens (GCA_000186865.1) (Aureococcus anophagefferens)

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

Reticulomyxa filosa (GCA_000512085.1) (Reticulomyxa filosa)

Plasmodiophora brassicae (GCA_001049375.1) (Plasmodiophora brassicae)

Bigelowiella natans (Bigelowiella natans CCMP2755)

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

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

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

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

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

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

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

Plasmodium gallinaceum (GCA_900005855.1) (Plasmodium gallinaceum)

Plasmodium relictum (GCA_900005765.1) (Plasmodium relictum)

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

Plasmodium berghei (Plasmodium berghei ANKA)

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

Plasmodium chabaudi (Plasmodium chabaudi chabaudi strain AS)

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

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

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

Plasmodium falciparum 3D7 (Plasmodium falciparum 3D7)

Plasmodium gaboni (GCA_001602025.1) (Plasmodium gaboni)

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

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

Plasmodium gonderi (GCA_002157705.1) (Plasmodium gonderi)

Plasmodium knowlesi (Plasmodium knowlesi strain H)

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

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

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

Plasmodium vivax (Plasmodium vivax strain Salvador I)

Plasmodium coatneyi (GCA_001680005.1) (Plasmodium coatneyi)

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

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

Eimeria brunetti (GCA_000499725.1) (Eimeria brunetti)

Eimeria mitis (GCA_000499745.1) (Eimeria mitis)

Eimeria acervulina (GCA_000499425.1) (Eimeria acervulina)

Eimeria praecox (GCA_000499445.1) (Eimeria praecox)

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)

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

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

Cryptosporidium andersoni (GCA_001865355.1) (Cryptosporidium andersoni)

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

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

Cryptosporidium ubiquitum (GCA_001865345.1) (Cryptosporidium ubiquitum)

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

Gregarina niphandrodes (GCA_000223845.4) (Gregarina niphandrodes)

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

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

Tetrahymena thermophila (Tetrahymena thermophila SB210)

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

Pseudocohnilembus persalinus (GCA_001447515.1) (Pseudocohnilembus persalinus)

Paramecium tetraurelia (Paramecium tetraurelia)

Stentor coeruleus (GCA_001970955.1) (Stentor coeruleus)

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

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

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

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

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

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

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

Emiliania huxleyi (Emiliania huxleyi CCMP1516)

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