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

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

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

Plasmodium gonderi (GCA_002157705.1) (Plasmodium gonderi)

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

Plasmodium knowlesi - GCA_000006355.3 (Plasmodium knowlesi strain H)

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

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

Plasmodium vivax - GCA_900093555.2 (Plasmodium vivax strain Salvador I)

Plasmodium falciparum - GCA_000002765.3 (Plasmodium falciparum 3D7)

Plasmodium gaboni (GCA_001602025.1) (Plasmodium gaboni)

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

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

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

Plasmodium berghei - GCA_900002375.2 (Plasmodium berghei ANKA)

Plasmodium chabaudi (Plasmodium chabaudi chabaudi strain AS)

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

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

Plasmodium gallinaceum (GCA_900005855.1) (Plasmodium gallinaceum)

Plasmodium relictum (GCA_900005765.1) (Plasmodium relictum)

Plasmodium coatneyi (GCA_001680005.1) (Plasmodium coatneyi)

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

Babesia bovis T2Bo - GCA_000165395.2 (Babesia bovis T2Bo)

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

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

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)

Eimeria acervulina (GCA_000499425.1) (Eimeria acervulina)

Eimeria brunetti (GCA_000499725.1) (Eimeria brunetti)

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

Eimeria mitis - GCA_000499745.2 (Eimeria mitis strain Houghton)

Eimeria praecox (GCA_000499445.1) (Eimeria praecox)

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

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

Toxoplasma gondii - GCA_000006565.2 (Toxoplasma gondii ME49)

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

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

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

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

Cryptosporidium andersoni (GCA_001865355.1) (Cryptosporidium andersoni)

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

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

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

Cryptosporidium ubiquitum (GCA_001865345.1) (Cryptosporidium ubiquitum)

Gregarina niphandrodes (GCA_000223845.4) (Gregarina niphandrodes)

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

Tetrahymena thermophila (Tetrahymena thermophila SB210)

Paramecium tetraurelia (Paramecium tetraurelia)

Pseudocohnilembus persalinus (GCA_001447515.1) (Pseudocohnilembus persalinus)

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

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

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)

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

Phytophthora parasitica (Phytophthora nicotianae P1569)

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

Phytophthora infestans (Phytophthora infestans T30-4)

Phytophthora kernoviae (Phytophthora kernoviae 00238/432)

Phytophthora lateralis (Phytophthora lateralis MPF4)

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

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

Phytophthora ramorum (Phytophthora ramorum)

Phytophthora sojae (Phytophthora sojae strain P6497)

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis Emoy2)

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)

Aphanomyces astaci - GCA_000520075.1 (Aphanomyces astaci strain strain APO3)

Aphanomyces invadans - GCA_000520115.1 (Aphanomyces invadans strain NJM9701)

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

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

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

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

Pythium irregulare (Globisporangium irregulare DAOM BR486)

Pythium iwayamai (Globisporangium iwayamae DAOM BR242034)

Pythium ultimum (Globisporangium ultimum DAOM BR144 pug)

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444)

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531)

Pythium vexans (Phytopythium vexans DAOM BR484)

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)

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)

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

Hondaea fermentalgiana (GCA_002897355.1) (Hondaea fermentalgiana)

Bigelowiella natans (Bigelowiella natans CCMP2755)

Plasmodiophora brassicae (GCA_001049375.1) (Plasmodiophora brassicae)

Reticulomyxa filosa (GCA_000512085.1) (Reticulomyxa filosa)

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)

Trypanosoma brucei (Trypanosoma brucei)

Trypanosoma equiperdum (GCA_001457755.2) (Trypanosoma equiperdum)

Trypanosoma conorhini (GCA_003719485.1) (Trypanosoma conorhini)

Trypanosoma theileri (GCA_002087225.1) (Trypanosoma theileri)

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

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

Angomonas deanei (GCA_000442575.2) (Angomonas deanei)

Strigomonas culicis (GCA_000442495.1) (Strigomonas culicis)

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

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

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

Entamoeba histolytica (Entamoeba histolytica HM-1:IMSS)

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

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

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

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

Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis strain WB C6)

Spironucleus salmonicida - GCA_000497125.2 (Spironucleus salmonicida strain ATCC 50377)

Kipferlia bialata (GCA_003568945.1) (Kipferlia bialata)

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

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

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

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

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

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

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

Guillardia theta CCMP2712 (Guillardia theta CCMP2712)

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

Emiliania huxleyi (Emiliania huxleyi CCMP1516)

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