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

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)

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)

Strigomonas culicis (GCA_000442495.1) (Strigomonas culicis)

Angomonas deanei (GCA_000442575.2) (Angomonas deanei)

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

Leishmania infantum (GCA_900500625.1) (Leishmania infantum)

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)

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

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

Trypanosoma equiperdum (GCA_001457755.2) (Trypanosoma equiperdum)

Trypanosoma brucei (Trypanosoma brucei)

Trypanosoma conorhini (GCA_003719485.1) (Trypanosoma conorhini)

Trypanosoma theileri (GCA_002087225.1) (Trypanosoma theileri)

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)

Dictyostelium discoideum (Dictyostelium discoideum AX4)

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

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

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

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)

Hondaea fermentalgiana (GCA_002897355.1) (Hondaea fermentalgiana)

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

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531)

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444)

Pythium iwayamai (Globisporangium iwayamae DAOM BR242034)

Pythium irregulare (Globisporangium irregulare DAOM BR486)

Pythium ultimum (Globisporangium ultimum DAOM BR144)

Pythium vexans (Phytopythium vexans DAOM BR484)

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

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

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

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

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

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

Phytophthora kernoviae (Phytophthora kernoviae 00238/432)

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

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

Phytophthora sojae (Phytophthora sojae strain P6497)

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

Phytophthora infestans (Phytophthora infestans T30-4)

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

Phytophthora parasitica (Phytophthora parasitica P1569)

Phytophthora lateralis (Phytophthora lateralis MPF4)

Phytophthora ramorum (Phytophthora ramorum)

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

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

Plasmopara halstedii (GCA_900000015.1) (Plasmopara halstedii)

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis Emoy2)

Albugo laibachii (Albugo laibachii Nc14)

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

Thalassiosira pseudonana (Thalassiosira pseudonana CCMP1335)

Pseudo-nitzschia multistriata (Pseudo-nitzschia multistriata)

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

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1)

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)

Plasmodiophora brassicae (GCA_001049375.1) (Plasmodiophora brassicae)

Bigelowiella natans (Bigelowiella natans CCMP2755)

Reticulomyxa filosa (GCA_000512085.1) (Reticulomyxa filosa)

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

Eimeria praecox (GCA_000499445.1) (Eimeria praecox)

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

Eimeria brunetti (GCA_000499725.1) (Eimeria brunetti)

Eimeria acervulina (GCA_000499425.1) (Eimeria acervulina)

Eimeria mitis (GCA_000499745.1) (Eimeria mitis)

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

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

Toxoplasma gondii ME49 (Toxoplasma gondii ME49)

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

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

Cryptosporidium andersoni (GCA_001865355.1) (Cryptosporidium andersoni)

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)

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 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)

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

Plasmodium gallinaceum (GCA_900005855.1) (Plasmodium gallinaceum)

Plasmodium relictum (GCA_900005765.1) (Plasmodium relictum)

Plasmodium chabaudi (Plasmodium chabaudi chabaudi strain AS)

Plasmodium berghei (Plasmodium berghei ANKA)

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

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

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

Plasmodium falciparum 3D7 (Plasmodium falciparum 3D7)

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

Plasmodium gaboni (GCA_001602025.1) (Plasmodium gaboni)

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

Plasmodium gonderi (GCA_002157705.1) (Plasmodium gonderi)

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

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

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

Plasmodium vivax (Plasmodium vivax strain Salvador I)

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

Plasmodium knowlesi (Plasmodium knowlesi strain H)

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

Plasmodium coatneyi (GCA_001680005.1) (Plasmodium coatneyi)

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)

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

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

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

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

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)