FAQs

1. How are the gene trees inferred?
• Maximum likelihood tree inference from a multiple sequence alignment is used: OrthoFinder version 3 is used to infer groups containing all homologous genes. The sequences for each database tree are aligned using MAFFT L-INS-i for up to 500 sequences or default MAFFT for larger alignments. Trees are inferred using FastTree with default parameters. This is performed by OrthoFinder, which also roots the tree using a rooted gene tree to identify the outgroup genes. A user's query gene is added to the alignment using MAFFT and is added to the pre-computed gene tree using RAxML's EPA. The user's tree is rooted on the same genes as the database tree.
2. How is the tree visualisation done?
• All credit is due to phlotree.js developed by Stephen D. Shank, Steven Weaver & Sergei L. Kosakovsky Pond (have I missed anyone?). It was very easy to use and looks great! The github page is here: https://github.com/veg/phylotree.js and the citation is:
  • Shank, S., Weaver, S. & Kosakovsky Pond, S. phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics. BMC Bioinformatics 19, 276 (2018). https://doi.org/10.1186/s12859-018-2283-2
3. How is SHOOT licensed?
• This work, including the data produced by SHOOT, is licensed under a CC BY 4.0 license.
4. How do we cite SHOOT?
• Emms, D.M., Kelly, S. SHOOT: phylogenetic gene search and ortholog inference. Genome Biol 23, 85 (2022). https://doi.org/10.1186/s13059-022-02652-8
5. Can I run SHOOT locally on my on databases?
• Yes, you can download the SHOOT command line application here: https://github.com/davidemms/SHOOT and you can create your own databases using OrthoFinder: https://github.com/davidemms/OrthoFinder, https://en.wikipedia.org/wiki/OrthoFinder.
6. What databases does SHOOT use?
• SHOOT offers a range of curated databases. The motivation for encouraging the use of curated databases over defaulting to the BLAST nr database is that these curated databases should make it easier to picture the evolution of the whole gene family rather than overwhelming the tree with thousands of near-identical hits. The current databases are:
• LUCA - A dataset with 78 species from across all domains of life
• Metazoa
• Bacteria & Archaea
• Fungi
• Plants
7. Could my tree need to be manually re-rooted?
• This is possible if your gene is an out-group to the species in the database you searched against. It's not possible to detect this programmatically so you should consider whether the tree should be re-rooted on your query gene. A far better approach is to search against a database which has a taxonomic range which covers your species. SHOOT should then be able to root the gene tree correctly. It isn't necessary for the database to actually contain your species.
8. Can we put SHOOT as a gene search tool on our genome resource website?
• Yes! Please get in touch and I'll help you get set up.
9. Database details:
• Fungi - view the Species Tree

  27 species across the Fungi kingdom plus 5 outgroup species. The proteomes are from Ensembl: https://fungi.ensembl.org.

Agaricus bisporus	Cryptococcus neoformans	Rhizoctonia solani
Amanita muscaria	Encephalitozoon intestinalis	Rhizopus delemar
Aspergillus fumigatus	Enterocytozoon bieneusi	Saccharomyces cerevisiae
Aspergillus nidulans	Fusarium oxysporum	Schizosaccharomyces pombe
Batrachochytrium salamandrivorans	Magnaporthe oryzae	Sclerotinia sclerotiorum
Blumeria graminis	Mortierella elongata	Spizellomyces punctatus
Botrytis cinerea	Neurospora crassa	Ustilago maydis
Candida albicans	Phaeosphaeria nodorum	Yarrowia lipolytica
Colletotrichum graminicola	Puccinia graminis	Zymoseptoria tritici

Outgroup species: Caenorhabditis elegans, Homo sapiens, Drosophila melanogaster (Metazoa), Dictyostelium discoideum (Amoeba) & Monosiga brevicollis (Choanoflagellate)

• Metazoa - view the Species Tree

  49 species across the Animal kingdom plus 5 outgroup species. The proteomes are from Ensembl: https://ensembl.org.

Amphimedon queenslandica	Danio rerio	Octopus bimaculoides
Anolis carolinensis	Daphnia magna	Oncorhynchus mykiss
Anopheles gambiae	Drosophila melanogaster	Ornithorhynchus anatinus
Apis mellifera	Gadus morhua	Oryzias latipes
Astatotilapia calliptera	Gallus gallus	Pan troglodytes
Bombyx mori	Glossina morsitans	Petromyzon marinus
Bos taurus	Helobdella robusta	Phascolarctos cinereus
Branchiostoma lanceolatum	Homo sapiens	Poecilia formosa
Bubo bubo	Ixodes scapularis	Rattus norvegicus
Caenorhabditis elegans	Latimeria chalumnae	Schistosoma mansoni
Callithrix jacchus	Lepisosteus oculatus	Strongylocentrotus purpuratus
Callorhinchus milii	Leptobrachium leishanense	Tetraodon nigroviridis
Canis familiaris	Mnemiopsis leidyi	Thelohanellus kitauei
Chrysemys picta	Monodelphis domestica	Trichinella spiralis
Ciona intestinalis	Mus musculus	Trichoplax adhaerens
Corvus moneduloides	Nematostella vectensis	Xenopus tropicalis
Crocodylus porosus

Outgroup species: Monosiga brevicollis (Choanoflagellate), Phaeosphaeria nodorum, Saccharomyces cerevisiae, Schizosaccharomyces pombe (Fungi) & Dictyostelium discoideum (Amoeba)

• Plants - view the Species Tree

  30 species across the Green Plants (Viridiplantae) plus 3 Red Algal outgroup species. The Green Plant proteomes are from Phytozome: https://phytozome.jgi.doe.gov and the Red Algae proteomes are from Ensembl: https://plants.ensembl.org.

Amborella trichopoda	Glycine max	Picea glauca
Anthoceros punctatus	Gossypium raimondii	Pinus sylvestris
Aquilegia coerulea	Hordeum vulgare	Prunus persica
Arabidopsis thaliana	Manihot esculenta	Selaginella moellendorffii
Azolla filiculoides	Marchantia polymorpha	Setaria italica
Brassica oleracea	Micromonas spRCC299	Solanum lycopersicum
Chara braunii	Musa acuminata	Spirodela polyrhiza
Chlamydomonas reinhardtii	Oryza sativa	Triticum aestivum
Eucalyptus grandis	Ostreococcus lucimarinus	Volvox carteri
Gingko biloba	Physcomitrella patens	Zea mays

Outgroup species: Chondrus crispus, Cyanidioschyzon merolae & Galdieria sulphuraria

• LUCA / UniProt - view the partially resolved Species Tree

This database contains 78 species across all domains of life from the UniProt Reference Proteomes 2020. UniProt says: "Reference proteomes have been selected among all proteomes (manually and algorithmically, according to a number of criteria) to provide broad coverage of the tree of life."

Eukaryota	Bacteria	Archaea
Anopheles gambiae	Aquifex aeolicus	Halobacterium salinarum
Arabidopsis thaliana	Bacillus subtilis	Korarchaeum cryptofilum
Batrachochytrium dendrobatidis	Bacteroides thetaiotaomicron	Methanocaldococcus jannaschii
Bos taurus	Bradyrhizobium diazoefficiens	Methanosarcina acetivorans
Branchiostoma floridae	Chlamydia trachomatis	Nitrosopumilus maritimus
Caenorhabditis elegans	Chloroflexus aurantiacus	Saccharolobus solfataricus
Candida albicans	Deinococcus radiodurans	Thermococcus kodakarensis
Canis lupus familiaris	Dictyoglomus turgidum
Chlamydomonas reinhardtii	Escherichia coli
Ciona intestinalis	Fusobacterium nucleatum
Cryptococcus neoformans	Geobacter sulfurreducens
Danio rerio	Gloeobacter violaceus
Dictyostelium discoideum	Helicobacter pylori
Drosophila melanogaster	Leptospira interrogans
Gallus gallus	Mycobacterium tuberculosis
Giardia intestinalis	Mycoplasma genitalium
Gorilla gorilla gorilla	Neisseria meningitidis
Helobdella robusta	Pseudomonas aeruginosa
Homo sapiens	Rhodopirellula baltica
Ixodes scapularis	Streptomyces coelicolor
Leishmania major	Synechocystis sp.
Lepisosteus oculatus	Thermodesulfovibrio yellowstonii
Monodelphis domestica	Thermotoga maritima
Monosiga brevicollis
Mus musculus
Nematostella vectensis
Neosartorya fumigata
Neurospora crassa
Oryza sativa subsp. japonica
Oryzias latipes
Pan troglodytes
Paramecium tetraurelia
Phaeosphaeria nodorum
Physcomitrella patens
Phytophthora ramorum
Plasmodium falciparum
Puccinia graminis
Rattus norvegicus
Saccharomyces cerevisiae
Schizosaccharomyces pombe
Sclerotinia sclerotiorum
Thalassiosira pseudonana
Tribolium castaneum
Trichomonas vaginalis
Ustilago maydis
Xenopus tropicalis
Yarrowia lipolytica
Zea mays

• Bacteria & Archaea - view the NCBI taxonomy here

This database contains 252 strains, with 56 strains selected for their scientific & medical importance and a further 196 strains selected using a phylogenetic sampling method to best represent the sequence diversity of all sequenced prokaryotes."

Uniprot proteome	NCBI taxon	Name in SHOOT	Selection
UP000000425	122586	Neisseria_meningitidis	QfO Uniprot ref. prot.
UP000000429	85962	Helicobacter_pylori	QfO Uniprot ref. prot.
UP000000431	272561	Chlamydia_trachomatis	QfO Uniprot ref. prot.
UP000000536	69014	Thermococcus_kodakarensis	QfO Uniprot ref. prot.
UP000000554	64091	Halobacterium_salinarum	QfO Uniprot ref. prot.
UP000000557	251221	Gloeobacter_violaceus	QfO Uniprot ref. prot.
UP000000577	243231	Geobacter_sulfurreducens	QfO Uniprot ref. prot.
UP000000625	83333	Escherichia_coli	QfO Uniprot ref. prot.
UP000000718	289376	Thermodesulfovibrio_yellowstonii	QfO Uniprot ref. prot.
UP000000792	436308	Nitrosopumilus_maritimus	QfO Uniprot ref. prot.
UP000000798	224324	Aquifex_aeolicus	QfO Uniprot ref. prot.
UP000000805	243232	Methanocaldococcus_jannaschii	QfO Uniprot ref. prot.
UP000000807	243273	Mycoplasma_genitalium	QfO Uniprot ref. prot.
UP000001025	243090	Rhodopirellula_baltica	QfO Uniprot ref. prot.
UP000001408	189518	Leptospira_interrogans	QfO Uniprot ref. prot.
UP000001414	226186	Bacteroides_thetaiotaomicron	QfO Uniprot ref. prot.
UP000001425	1111708	Synechocystis_Kazusa	QfO Uniprot ref. prot.
UP000001570	224308	Bacillus_subtilis	QfO Uniprot ref. prot.
UP000001584	83332	Mycobacterium_tuberculosis	QfO Uniprot ref. prot.
UP000001686	374847	Korarchaeum_cryptofilum	QfO Uniprot ref. prot.
UP000001973	100226	Streptomyces_coelicolor	QfO Uniprot ref. prot.
UP000001974	273057	Saccharolobus_solfataricus	QfO Uniprot ref. prot.
UP000002008	324602	Chloroflexus_aurantiacus	QfO Uniprot ref. prot.
UP000002438	208964	Pseudomonas_aeruginosa	QfO Uniprot ref. prot.
UP000002487	188937	Methanosarcina_acetivorans	QfO Uniprot ref. prot.
UP000002521	190304	Fusobacterium_nucleatum	QfO Uniprot ref. prot.
UP000002524	243230	Deinococcus_radiodurans	QfO Uniprot ref. prot.
UP000002526	224911	Bradyrhizobium_diazoefficiens	QfO Uniprot ref. prot.
UP000007719	515635	Dictyoglomus_turgidum	QfO Uniprot ref. prot.
UP000008183	243274	Thermotoga_maritima	QfO Uniprot ref. prot.
UP000000265	272620	Klebsiella_pneumoniae	Highly cited
UP000000579	71421	Haemophilus_influenzae	Highly cited
UP000000580	262316	Mycolicibacterium_paratuberculosis	Highly cited
UP000000584	243277	Vibrio_cholerae	Highly cited
UP000000586	171101	Streptococcus_pneumoniae	Highly cited
UP000000588	242619	Porphyromonas_gingivalis	Highly cited
UP000000609	272624	Legionella_pneumophila	Highly cited
UP000000799	192222	Campylobacter_jejuni	Highly cited
UP000000813	176299	Agrobacterium_fabrum	Highly cited
UP000000815	632	Yersinia_pestis	Highly cited
UP000000817	169963	Listeria_monocytogenes	Highly cited
UP000000818	195102	Clostridium_perfringens	Highly cited
UP000001006	623	Shigella_flexneri	Highly cited
UP000001014	99287	Salmonella_typhimurium	Highly cited
UP000001978	272563	Clostridioides_difficile	Highly cited
UP000002196	272623	Lactococcus_lactis	Highly cited
UP000002256	395491	Rhizobium_leguminosarum	Highly cited
UP000006381	272621	Lactobacillus_acidophilus	Highly cited
UP000007477	871585	Acinetobacter_calcoaceticus	Highly cited
UP000008319	529507	Proteus_mirabilis	Highly cited
UP000008816	93061	Staphylococcus_aureus	Highly cited
UP000014594	1260356	Enterococcus_faecalis	Highly cited
UP000075229	140	Borrelia_hermsii	Highly cited
UP000198289	615	Serratia_marcescens	Highly cited
UP000028936	1528098	Rickettsiales_bacterium	Mitochondrion relative
UP000180235	1188229	Gloeomargarita_lithophora	Chloroplast  relative
UP000000543	279808	Staphylococcus_haemolyticus	Phylo. sampling
UP000000547	167879	Colwellia_psychrerythraea	Phylo. sampling
UP000000645	232721	Acidovorax_JS42	Phylo. sampling
UP000001169	272569	Haloarcula_marismortui	Phylo. sampling
UP000001361	883	Desulfovibrio_vulgaris	Phylo. sampling
UP000001362	243159	Acidithiobacillus_ferrooxidans	Phylo. sampling
UP000001961	64471	Synechococcus_CC9311	Phylo. sampling
UP000002011	471854	Dyadobacter_fermentans	Phylo. sampling
UP000002139	448385	Sorangium_cellulosum	Phylo. sampling
UP000002145	203119	Hungateiclostridium_thermocellum	Phylo. sampling
UP000002148	388919	Streptococcus_sanguinis	Phylo. sampling
UP000002208	546414	Deinococcus_deserti	Phylo. sampling
UP000002257	395965	Methylocella_silvestris	Phylo. sampling
UP000002386	471223	Geobacillus_WCH70	Phylo. sampling
UP000002457	521011	Methanosphaerula_palustris	Phylo. sampling
UP000002495	235279	Helicobacter_hepaticus	Phylo. sampling
UP000003277	742743	Dialister_succinatiphilus	Phylo. sampling
UP000003415	469616	Fusobacterium_mortiferum	Phylo. sampling
UP000003446	661087	Olsenella_F0356	Phylo. sampling
UP000003855	665956	Subdoligranulum_4-3-54A2FAA	Phylo. sampling
UP000003981	621372	Paenibacillus_D14	Phylo. sampling
UP000004073	1105031	Clostridium_MSTE9	Phylo. sampling
UP000004090	428127	Absiella_dolichum	Phylo. sampling
UP000004259	246199	Ruminococcus_albus	Phylo. sampling
UP000004478	1225176	Cecembia_lonarensis	Phylo. sampling
UP000004870	638300	Cardiobacterium_hominis	Phylo. sampling
UP000005262	768704	Desulfosporosinus_meridiei	Phylo. sampling
UP000006229	1131455	Mycoplasma_canis	Phylo. sampling
UP000006415	857290	Scardovia_wiggsiae	Phylo. sampling
UP000006556	370438	Pelotomaculum_thermopropionicum	Phylo. sampling
UP000006743	557723	Haemophilus_parasuis	Phylo. sampling
UP000007271	1185325	Lactobacillus_coryniformis	Phylo. sampling
UP000007753	452662	Sphingobium_japonicum	Phylo. sampling
UP000007995	997888	Bacteroides_finegoldii	Phylo. sampling
UP000008204	41431	Rippkaea_orientalis	Phylo. sampling
UP000008212	243275	Treponema_denticola	Phylo. sampling
UP000008308	263358	Micromonospora_maris	Phylo. sampling
UP000008701	290317	Chlorobium_phaeobacteroides	Phylo. sampling
UP000009044	634177	Komagataeibacter_medellinensis	Phylo. sampling
UP000009154	1112204	Gordonia_polyisoprenivorans	Phylo. sampling
UP000011615	1230457	Haloterrigena_limicola	Phylo. sampling
UP000011728	931276	Clostridium_saccharoperbutylacetonicum	Phylo. sampling
UP000013232	1123367	Thauera_linaloolentis	Phylo. sampling
UP000017993	1262970	Subdoligranulum_CAG314	Phylo. sampling
UP000018014	1262708	Bacillus_CAG988	Phylo. sampling
UP000018042	1262875	Eggerthella_CAG209	Phylo. sampling
UP000018237	1262989	Firmicutes_bacterium	Phylo. sampling
UP000018329	1262693	Alistipes_CAG268	Phylo. sampling
UP000018361	1263102	Prevotella_copri	Phylo. sampling
UP000018415	1341679	Acinetobacter_indicus	Phylo. sampling
UP000019028	1239307	Sodalis_praecaptivus	Phylo. sampling
UP000019082	1302241	Cutibacterium_acnes	Phylo. sampling
UP000019222	1224164	Corynebacterium_vitaeruminis	Phylo. sampling
UP000019267	1276246	Spiroplasma_culicicola	Phylo. sampling
UP000020878	1454005	Candidatus_Accumulibacter	Phylo. sampling
UP000028780	156978	Corynebacterium_imitans	Phylo. sampling
UP000028875	1462526	Virgibacillus_massiliensis	Phylo. sampling
UP000029622	1156417	Caloranaerobacter_azorensis	Phylo. sampling
UP000030960	561184	Mameliella_alba	Phylo. sampling
UP000031057	1348853	Novosphingobium_malaysiense	Phylo. sampling
UP000031627	1410383	Candidatus_Tachikawaea	Phylo. sampling
UP000032279	1335616	Paucilactobacillus_wasatchensis	Phylo. sampling
UP000032287	137591	Weissella_cibaria	Phylo. sampling
UP000033511	43662	Pseudoalteromonas_piscicida	Phylo. sampling
UP000036114	1628212	Chromobacterium_LK11	Phylo. sampling
UP000036921	1581033	Bacillus_FJAT-21945	Phylo. sampling
UP000037530	171383	Vibrio_hepatarius	Phylo. sampling
UP000037870	1592329	Actinobacteria_bacterium	Phylo. sampling
UP000044377	1109412	Brenneria_goodwinii	Phylo. sampling
UP000050971	1736540	Aeromicrobium_Root472D3	Phylo. sampling
UP000051467	1736232	Arthrobacter_Leaf69	Phylo. sampling
UP000051585	1736381	Aureimonas_Leaf454	Phylo. sampling
UP000051643	270918	Salegentibacter_mishustinae	Phylo. sampling
UP000051802	676599	Stenotrophomonas_panacihumi	Phylo. sampling
UP000053086	1700846	Lysinibacillus_F5	Phylo. sampling
UP000054024	146536	Streptomyces_curacoi	Phylo. sampling
UP000054457	1685377	Microbulbifer_ZGT114	Phylo. sampling
UP000057134	1766	Mycolicibacterium_fortuitum	Phylo. sampling
UP000058305	412690	Microterricola_viridarii	Phylo. sampling
UP000061489	1420916	Marinobacter_similis	Phylo. sampling
UP000065824	1702325	Chelatococcus_CO-6	Phylo. sampling
UP000070463	1698267	Candidate_MSBL1-archaeon	Phylo. sampling
UP000077018	683316	Frankia_EI5c	Phylo. sampling
UP000077275	47311	Methanobrevibacter_cuticularis	Phylo. sampling
UP000077319	1822215	Erythrobacter_HI00D59	Phylo. sampling
UP000093220	189873	Bradyrhizobium_LMTRsp-3	Phylo. sampling
UP000093585	319501	Brevibacillus_WF146	Phylo. sampling
UP000094329	1891921	Piscirickettsia_litoralis	Phylo. sampling
UP000094487	1888892	Sphingomonas_turrisvirgatae	Phylo. sampling
UP000094689	1842539	Bosea_RAC05	Phylo. sampling
UP000095256	762845	Enterococcus_rivorum	Phylo. sampling
UP000176615	1739315	Globicatella_HMSC072A10	Phylo. sampling
UP000182624	43305	Butyrivibrio_proteoclasticus	Phylo. sampling
UP000184455	1855338	Nitrosospira_Nsp11	Phylo. sampling
UP000184520	634436	Marisediminitalea_aggregata	Phylo. sampling
UP000186096	58117	Microbispora_rosea	Phylo. sampling
UP000186602	1261634	Roseburia_sp499	Phylo. sampling
UP000187327	1883416	Halomonas_sp1513	Phylo. sampling
UP000187995	1805827	Rhodococcus_MTM3W5	Phylo. sampling
UP000190286	745368	Gemmiger_formicilis	Phylo. sampling
UP000191905	1873176	Pseudaminobacter_manganicus	Phylo. sampling
UP000192042	1325564	Nitrospira_japonica	Phylo. sampling
UP000193006	199441	Alkalihalobacillus_krulwichiae	Phylo. sampling
UP000193136	1969733	Geothermobacter_EPR-M	Phylo. sampling
UP000194216	1985172	Sphingomonas_IBVSS2	Phylo. sampling
UP000194221	1635173	Tenacibaculum_holothuriorum	Phylo. sampling
UP000195076	1932621	Nostoc_T09	Phylo. sampling
UP000195161	1929267	Flavobacterium_FPG59	Phylo. sampling
UP000195529	1965622	Megasphaera_An286	Phylo. sampling
UP000195781	1232426	Collinsella_massiliensis	Phylo. sampling
UP000197446	431059	Pelomonas_puraquae	Phylo. sampling
UP000198589	1798228	Blastococcus_DSMsp-46838	Phylo. sampling
UP000198953	46177	Nonomuraea_pusilla	Phylo. sampling
UP000199067	1780377	Coriobacteriaceae_bacterium	Phylo. sampling
UP000199242	1141221	Chryseobacterium_taihuense	Phylo. sampling
UP000199432	1882749	Opitutus_GAS368	Phylo. sampling
UP000199671	332524	Actinomyces_ruminicola	Phylo. sampling
UP000199705	551996	Mucilaginibacter_gossypii	Phylo. sampling
UP000199768	1881066	Phyllobacterium_YR620	Phylo. sampling
UP000199802	1965654	Lachnoclostridium_An76	Phylo. sampling
UP000202922	1524263	Confluentimicrobium_lipolyticum	Phylo. sampling
UP000215509	554312	Paenibacillus_rigui	Phylo. sampling
UP000216308	1383851	Halorubrum_halodurans	Phylo. sampling
UP000217076	83401	Roseospirillum_parvum	Phylo. sampling
UP000217289	1294270	Melittangium_boletus	Phylo. sampling
UP000221394	442709	Flavimobilis_soli	Phylo. sampling
UP000222106	638953	Georgenia_soli	Phylo. sampling
UP000230810	2049589	Pseudomonas_HLS-6	Phylo. sampling
UP000232878	2058137	Polaribacter_ALD11	Phylo. sampling
UP000232889	1250229	Ulvibacter_MAR-2010-11	Phylo. sampling
UP000235352	2029108	Bacillus_UMB0899	Phylo. sampling
UP000236356	2067550	Clostridium_chh4-2	Phylo. sampling
UP000236731	797291	Sphingobacterium_lactis	Phylo. sampling
UP000238164	75385	Micropruina_glycogenica	Phylo. sampling
UP000238375	1469603	Spirosoma_oryzae	Phylo. sampling
UP000243063	1245526	Pseudomonas_guangdongensis	Phylo. sampling
UP000243494	2020948	Romboutsia_maritimum	Phylo. sampling
UP000244224	589035	Gemmobacter_caeni	Phylo. sampling
UP000245108	2108523	Lawsonibacter_asaccharolyticus	Phylo. sampling
UP000245507	2201891	Nocardioides_silvaticus	Phylo. sampling
UP000245623	2173179	Microbacterium_4-13	Phylo. sampling
UP000245926	2202825	Methylobacterium_durans	Phylo. sampling
UP000247832	670078	Arthrobacter_livingstonensis	Phylo. sampling
UP000249065	2230885	Roseicella_frigidaeris	Phylo. sampling
UP000250434	1804986	Amycolatopsis_albispora	Phylo. sampling
UP000252733	989	Marinilabilia_salmonicolor	Phylo. sampling
UP000253318	1931232	Marinitenerispora_sediminis	Phylo. sampling
UP000254875	2211104	Paraburkholderia_lacunae	Phylo. sampling
UP000260665	2184758	Rhodoferax_IMCC26218	Phylo. sampling
UP000265971	1825976	Neorhizobium_NCHU2750	Phylo. sampling
UP000266860	1630648	Novosphingobium_MD-1	Phylo. sampling
UP000269803	2485200	Frondihabitans_PhB188	Phylo. sampling
UP000273083	1329262	Mobilisporobacter_senegalensis	Phylo. sampling
UP000275325	2495580	Sphingomonas_TF3	Phylo. sampling
UP000276437	1930071	Methylomusa_anaerophila	Phylo. sampling
UP000279089	1647451	Chitinophaga_barathri	Phylo. sampling
UP000282084	2072	Saccharothrix_australiensis	Phylo. sampling
UP000287188	2014872	Dictyobacter_kobayashii	Phylo. sampling
UP000287890	2507159	Clostridium_JN-9	Phylo. sampling
UP000288096	45657	Desulfonema_ishimotonii	Phylo. sampling
UP000288291	2495899	Lactobacillus_xujianguonis	Phylo. sampling
UP000288967	2501295	Dyella_M7H15-1	Phylo. sampling
UP000289784	2137479	Pseudoxanthomonas_composti	Phylo. sampling
UP000292120	2528630	Aquabacterium_KMB7	Phylo. sampling
UP000294096	2510646	Loktanella_IMCC34160	Phylo. sampling
UP000294498	1539049	Dinghuibacter_silviterrae	Phylo. sampling
UP000295707	1537524	Thiogranum_longum	Phylo. sampling
UP000297351	2561925	Brevundimonas_S30B	Phylo. sampling
UP000306069	2040651	Campylobacter_12-5580	Phylo. sampling
UP000307244	2571272	Pedobacter_RP-3-15	Phylo. sampling
UP000307467	343240	Thiotrophic_endosymbiont	Phylo. sampling
UP000307507	2565924	Flavobacterium_CC-CTC003	Phylo. sampling
UP000307657	2565367	Lacinutrix_CAUsp-1491	Phylo. sampling
UP000315440	2527991	Pseudobythopirellula_maris	Phylo. sampling
UP000316225	384678	Paracoccus_sulfuroxidans	Phylo. sampling
UP000316304	2528004	Novipirellula_galeiformis	Phylo. sampling
UP000318165	92402	Mycoplasma_equirhinis	Phylo. sampling
UP000318431	1036180	Massilia_lurida	Phylo. sampling
UP000318566	2768454	Streptomyces_SLBN-118	Phylo. sampling
UP000319173	713054	TM7_phylum	Phylo. sampling
UP000322791	2606448	Hymenobacter_KIGAM108	Phylo. sampling
UP000324880	1948890	Rhodobacterales_bacterium	Phylo. sampling
UP000325372	2613842	Wenzhouxiangella_W260	Phylo. sampling
UP000326711	2487892	Corynebacterium_LMM-1652	Phylo. sampling
UP000326944	2590022	Sulfurimonas_GYSZ1	Phylo. sampling
UP000437955	2653936	Tetrasphaera_F2B08	Phylo. sampling
UP000441772	2650774	Bifidobacterium_LMGsp-31471	Phylo. sampling
UP000462055	2650748	Actinomadura_LD22	Phylo. sampling
UP000474632	2710884	Parapusillimonas_SGNA-6	Phylo. sampling
UP000476210	343235	Methanotrophic_endosymbiont	Phylo. sampling
UP000477884	2703788	Edaphobacter_12200R-103	Phylo. sampling
UP000481552	2706104	Streptomyces_SID8455	Phylo. sampling
UP000500686	754515	Mycoplasma_ES2806-GEN	Phylo. sampling
UP000502894	2708020	Legionella_TUM19329	Phylo. sampling
UP000503441	2714933	Leucobacter_HDW9A	Phylo. sampling
UP000505377	2736640	Pseudonocardia_broussonetiae	Phylo. sampling

10. Some gene trees in the database have been temporarily inferred using FastTree while waiting for the IQ-TREE trees to finish:

Database	Fungi	Metazoa	Plants	UniProt	Bacteria & Archaea
Trees in database	9115	10516	10617	17124	16156
FastTree used (tree IDs)	-	0, 1	0	0	0