Dataset Open Access

Phylogenomic analyses of 142 prokaryotic genera

Alexis Criscuolo

This repository contains 142 tar archive files, each corresponding to a prokaryotic genus. Each archive contains the following files/directories:

  • accn.tax.tsv           a tab-delimited file containing the assembly accession (col 1) and an associated taxon name (col 2) for each selected genome (one per line)
  • gff/                   a directory containing a gzip-compressed GFF3 file (as returned by the annotation tool Prokka) for each genome specified in accn.tax.tsv
  • cds.fna.gz             a gzip-compressed FASTA file containing all the coding sequences (at the codon level) from the GFF3 files in the directory gff/
  • msa/                   a directory containing multiple amino acid and codon sequence alignments (compressed FASTA files with extensions .afa.gz and .afc.gz, respectively) for each cluster of at least four homologous sequences (as determined by the pipeline Roary from the GFF3 files in gff/)
  • supermatrix.fasta.gz   a gzip-compressed FASTA file obtained by concatenating all the multiple codon sequence alignments in the directory msa/
  • tree.nwk               a Newick-formatted file containing a maximum-likelihood (ML) phylogenetic tree inferred from the file supermatrix.fasta.gz using IQ-TREE
  • iqtree.txt             a txt file summarizing the ML estimates of the GTR+Γ evolutionary model parameters, as returned by IQ-TREE when inferring the phylogenetic tree tree.nwk

 

A summary of the 142 phylogenomic analyses can be found in the tab-delimited file GTR.params.tree.tsv. Each line corresponds to one genus and contains the 12 following fields:
  [1]     genus name,
  [2-5]   frequencies of T, C, A, G, respectively,
  [6-10]  C-T, A-T, G-T, A-C, C-G rate parameters, respectively (normalized such that A-G rate = 1),
  [11]    Γ shape parameter alpha,
  [12]    Newick-formatted phylogenetic tree.

_____

Criscuolo A (2020) On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference. F1000Research, 9:1309. doi:10.12688/f1000research.26930.1

Files (19.9 GB)
Name Size
Acetobacter.tar
md5:8af2b4df0a104638c62ef778cb08ff29
87.2 MB Download
Achromobacter.tar
md5:0aa07fe72ed8e83d3306e71c0e0111db
180.2 MB Download
Acidovorax.tar
md5:496d66d3388f2b76f98f965ba6d0b02f
182.1 MB Download
Actinomyces.tar
md5:2cd2c52dfb0dc52044fb4e05fda1cc43
135.3 MB Download
Aerococcus.tar
md5:b634e352ab28b6700b270af1ab46230d
32.3 MB Download
Aeromonas.tar
md5:3dfed8e55201e9e0841681a5da2ed860
152.4 MB Download
Agrobacterium.tar
md5:2b31b33d260274599e224c099f59e6f5
170.4 MB Download
Alcanivorax.tar
md5:750881ab5263d4834c6c680545aaa136
50.6 MB Download
Alistipes.tar
md5:59ae4574804d36b051b2e7376ab6666a
45.3 MB Download
Alteromonas.tar
md5:17312c9fafec3b61da15a042aa6ba623
79.4 MB Download
Amycolatopsis.tar
md5:9841a3a3f95ca532e5c46d2af794bd1d
395.3 MB Download
Anaerococcus.tar
md5:7e890e0d8a605265e2fe37750d76eb09
37.2 MB Download
Anoxybacillus.tar
md5:2ebb2c68ed72af27004fe40fa5b4b785
40.4 MB Download
Arcobacter.tar
md5:345156d0fcce784bf82aa6c566a06a64
62.6 MB Download
Arthrobacter.tar
md5:3b451973ac836b5406d83d5c113dd954
522.0 MB Download
Azospirillum.tar
md5:1ffabc9f940e005745c292e343e4672e
131.4 MB Download
Bartonella.tar
md5:756af7fc82001efc17c5f672f5a2c7e4
67.6 MB Download
Blautia.tar
md5:b897d8910fa9623b2a8dcbbcbc48cf2d
76.7 MB Download
Brachyspira.tar
md5:a2a3b105d7052097bbc6f39c3c9b036c
33.5 MB Download
Bradyrhizobium.tar
md5:618dce72d0f5fe824ce5bf2f54c12e88
756.3 MB Download
Brevibacillus.tar
md5:c8ba0c4c43c8278aaad7a78ae90d85df
117.6 MB Download
Brevibacterium.tar
md5:fae13589acf76159aba444dbe2f782a4
66.2 MB Download
Brevundimonas.tar
md5:81540cd19e72d1b544d7fc10940e836a
76.0 MB Download
Butyrivibrio.tar
md5:795eb3d83640209db2b20c06913bb4c6
134.1 MB Download
Caballeronia.tar
md5:091d96cef9337ab6739b1945d635800f
242.7 MB Download
Capnocytophaga.tar
md5:4918c1c1186fa54a73930acebf926041
39.1 MB Download
Carnobacterium.tar
md5:e4d5bb71337c921b3afef521b3eeba18
35.7 MB Download
Caulobacter.tar
md5:2cd5922dd21e5e1cba3766526a40b6ab
141.3 MB Download
Chitinophaga.tar
md5:69bd11c460bc175903a6c786d75537cd
178.5 MB Download
Chromobacterium.tar
md5:6718b2feed8fb782ed193719fcb4fadb
64.2 MB Download
Chryseobacterium.tar
md5:6e1f492690a0c801f823e7d4636efc43
564.8 MB Download
Citrobacter.tar
md5:909f57d0a4e29f889c4e46b4413f6f84
102.5 MB Download
Clavibacter.tar
md5:a94384af6bcd8b62000cd56c6e820a8d
38.5 MB Download
Collinsella.tar
md5:5f68515fdd0d47a03758d795acda9cf1
39.1 MB Download
Comamonas.tar
md5:4bda58bc5d600d1091bea7b3c461b99d
60.4 MB Download
Cryobacterium.tar
md5:74dbecdc2b61e0f039fdefc5ae2c6931
80.5 MB Download
Cupriavidus.tar
md5:df2112580b41471263e735cb1f6f9e60
218.6 MB Download
Curtobacterium.tar
md5:468edf3d8785da6c03bdf760cb1f769c
110.9 MB Download
Deinococcus.tar
md5:5769b953fcc2fa1936afe86418926b6a
130.0 MB Download
Desulfovibrio.tar
md5:09546d677a5523180cc74f16d9e46bae
129.7 MB Download
Devosia.tar
md5:012ccad1cc6b004301945ddd4ed84ab1
104.8 MB Download
Dickeya.tar
md5:40f89254c727f24b1e681dd203dc5198
53.9 MB Download
Duganella.tar
md5:db126d1658937962e17b676472c1bfb5
87.3 MB Download
Ensifer.tar
md5:308fbfe1d2ca19efebcbee8fb903715a
149.0 MB Download
Erwinia.tar
md5:adc958744cd99d0c670554a6db04561a
79.8 MB Download
Erythrobacter.tar
md5:9062936e06c41b872165d9e903ffa1d0
86.6 MB Download
Eubacterium.tar
md5:184f90bb71b7aadf4f48e57c38598206
81.2 MB Download
Exiguobacterium.tar
md5:915aedf43209501391923a102e315502
66.8 MB Download
Faecalibacterium.tar
md5:bb6d8b8aad7742eaa28d8715c6a04155
28.8 MB Download
Fibrobacter.tar
md5:34a25fe327177c55fa31ee207550656c
67.7 MB Download
Flavobacterium.tar
md5:a427c60d4151c6815a3882cfc7497c5d
650.6 MB Download
Francisella.tar
md5:1197ddfcf03ba0dfa3e542db33cea71b
26.1 MB Download
Frankia.tar
md5:c5869aaf8f5d6d384fc4728197904489
118.6 MB Download
Fusobacterium.tar
md5:58b3f01eb5433d6d3227baa02b37cffb
49.2 MB Download
Gardnerella.tar
md5:023c8ca3d749f86ec54c5726d0373a77
15.6 MB Download
Geobacillus.tar
md5:f391fbf055bd7621c8f6ab5e17c86e8c
49.8 MB Download
Gilliamella.tar
md5:7cfa8503aae8d7c67b858f1a19ea198d
54.7 MB Download
Gluconobacter.tar
md5:dead24190eebe678dc5e0fa7c321036e
37.0 MB Download
Gordonia.tar
md5:84f67ac1a101b9c0bd4df81a21e7dbf9
153.0 MB Download
GTR.params.trees.tsv
md5:c955065c250fca5e844f2328ab58da14
362.1 kB Download
Haloferax.tar
md5:93c268bf4cddb0f5df03f1a23cbd74ce
44.2 MB Download
Halomonas.tar
md5:886c591b40ad6564b03164a1320868a6
346.1 MB Download
Halorubrum.tar
md5:78aa9c2d497bbd1701f8d6c812ad122e
84.6 MB Download
Herbaspirillum.tar
md5:a752ae178c7b4cfdc651dbaec1c2e86c
106.5 MB Download
Hymenobacter.tar
md5:3e6c96fb888d6946f2ecdeac2ca7f9df
149.9 MB Download
Janthinobacterium.tar
md5:84e0f1212402843b72a4ed692020f440
151.7 MB Download
Kocuria.tar
md5:3eb90f073e8649d2a70677fbf1d9ddf6
44.9 MB Download
Komagataeibacter.tar
md5:f3d83c118ace8932d6bb55d722d20d3d
55.8 MB Download
Lactococcus.tar
md5:b6b1073c0dadd8b4344faec7c683be5c
38.4 MB Download
Leifsonia.tar
md5:f22516a63c02965b2c3dac1792d411f9
70.4 MB Download
Leuconostoc.tar
md5:1c18d7020902d1258051eba9416f3718
17.9 MB Download
Limnohabitans.tar
md5:f45983fe6bf8b166f3a21a1ebccef8e5
99.1 MB Download
Lysinibacillus.tar
md5:2cbf5a3171e4255b162d8c3703104989
129.4 MB Download
Lysobacter.tar
md5:7185892ec088261038af6b042bcdc4e2
92.7 MB Download
Marinobacter.tar
md5:ce7d5ef7efb167ebb99c97f709e7e4a7
220.5 MB Download
Marinomonas.tar
md5:b1abc655971b64d6d133c1117b54c167
99.9 MB Download
Massilia.tar
md5:ec80f727857417f452cd3cad236175f2
175.4 MB Download
Megasphaera.tar
md5:4000bb693a666d473bf14b8a8419d8cc
28.7 MB Download
Mesorhizobium.tar
md5:d4c6216fa1d70c10355f862ef1e344d8
438.5 MB Download
Methanobrevibacter.tar
md5:38d8020d8472212858193ef7ce8ac489
27.2 MB Download
Methanosarcina.tar
md5:d79afb2d098cfa31c45885c169594a97
55.3 MB Download
Methylobacterium.tar
md5:2ca50f45647e90dd5c2de00a08ad4bbf
273.5 MB Download
Microbacterium.tar
md5:5f165835c19ea802bdb72c8e4d79ceaa
387.1 MB Download
Micromonospora.tar
md5:dd7e95a03ba9cc9db8aa1cc5f81bfafa
418.1 MB Download
Moraxella.tar
md5:a8d9075afa920773192c9cc1b10f1e78
42.9 MB Download
Mucilaginibacter.tar
md5:6746d3534c5ec43760e80eb7ad0e4ba4
179.5 MB Download
Mycolicibacterium.tar
md5:252168ea93f9594306d9d3a1d77584f6
477.1 MB Download
Nitrosomonas.tar
md5:bc01af2701283adf2001f979153643a4
78.9 MB Download
Nocardia.tar
md5:0220ba435c6f906370e46f953168cad1
629.3 MB Download
Nocardioides.tar
md5:949c328597f58e4d0b6756ea7db4c73c
177.4 MB Download
Nocardiopsis.tar
md5:4ac4b2a08b89b34571473e83e7da36ee
146.4 MB Download
Novosphingobium.tar
md5:7abf9e6f1ef7f9034b3917c413947d00
176.8 MB Download
Ochrobactrum.tar
md5:fa297be59624f5907ace17429da2d51e
88.6 MB Download
Olsenella.tar
md5:710eb6378ddbb741e018625758c98c3a
38.3 MB Download
Pandoraea.tar
md5:798e1f48f6b79f9afdab3add36ee54e0
79.5 MB Download
Pantoea.tar
md5:1589e6d5f5da98083cbbf52fd9ebe394
182.1 MB Download
Parabacteroides.tar
md5:4d5e959fdc9d89f2d0006fb6ba9e61b7
85.6 MB Download
Paraburkholderia.tar
md5:6a7a2a11874a64831e803322d6fa493e
559.1 MB Download
Paracoccus.tar
md5:69d3de37f6b5057b87b2bbf0f3296950
168.9 MB Download
Pectobacterium.tar
md5:3d7b9f6685a68db9df68b772c76a74d9
65.6 MB Download
Pediococcus.tar
md5:f2642f83ff3d0163aea0319423639aa1
19.8 MB Download
Pedobacter.tar
md5:93b0945bb7ca1f61b7d972b241abdf3c
308.6 MB Download
Peptoniphilus.tar
md5:89c490fca24cd0b0025438d18c2fcea4
39.5 MB Download
Phaeobacter.tar
md5:eb9be342176c49806d0b67e01cfed363
48.5 MB Download
Photobacterium.tar
md5:72b5a4fe5dc5b30c6fc949332520ffe4
173.6 MB Download
Photorhabdus.tar
md5:2bc0fa9105a59cc9675c2bbe356d4a6e
55.5 MB Download
Polynucleobacter.tar
md5:74657cdcc7f24ab44cf644ca28281df0
61.8 MB Download
Porphyromonas.tar
md5:2baccf3df119786e5bc2fcd9a06e408f
33.6 MB Download
Prevotella.tar
md5:2a20437311cb37f6e36c305ed9e347cd
250.9 MB Download
Prochlorococcus.tar
md5:8a5a71bbe266b897f26fb39079f8bf54
60.7 MB Download
Propionibacterium.tar
md5:27e1b83448d324538fa2aca8fa3cc8f4
26.1 MB Download
Proteus.tar
md5:d53366be60c8292ef04bcb169e01c73f
45.5 MB Download
Providencia.tar
md5:25ab16baa08e622f57f953a31602af38
57.1 MB Download
Pseudoalteromonas.tar
md5:ef033b0635c010109bb2c68cc3d148f0
290.5 MB Download
Pseudonocardia.tar
md5:32d94210ab38625889d24ceb69a36863
99.5 MB Download
Psychrobacter.tar
md5:8647f76c5ae9cc605fbe4aa639ed891a
88.6 MB Download
Ralstonia.tar
md5:8e5202d1098edcbf7b11fc75a2979b62
75.2 MB Download
Rhizobium.tar
md5:1d23d530411d2450f98d2dcd04cbb157
855.9 MB Download
Rhodobacter.tar
md5:b7c7bbdb57efd9dbf1fc942c7f488f52
60.9 MB Download
Roseburia.tar
md5:b4cc6c8fb30169938134f04a76592e7c
33.0 MB Download
Roseovarius.tar
md5:b47d38c30a424cd3c263dced0415697c
105.7 MB Download
Ruegeria.tar
md5:4e5e880af2da8395dbae1086c5ebb746
114.0 MB Download
Ruminococcus.tar
md5:8265a4654d44c2c5b0917c98ec4fd2ec
137.9 MB Download
Selenomonas.tar
md5:dc4cdb0cc80cbf3889df12e580762318
68.0 MB Download
Shewanella.tar
md5:57a50e5b2ba879ac3843a9ee3d26fc72
200.3 MB Download
Sinorhizobium.tar
md5:5193d5ab7dc23c23906405a41f0ad579
107.1 MB Download
Sphingobacterium.tar
md5:11773da72014f135f1c4c92921a78b96
144.9 MB Download
Sphingobium.tar
md5:5a7f4e5c569502c965f958378a556f50
181.5 MB Download
Sphingomonas.tar
md5:934360ed2ba476dc6047b8bd43113905
494.1 MB Download
Sphingopyxis.tar
md5:742b5d1ff6c790ccf843de17947b3936
136.8 MB Download
Spiroplasma.tar
md5:fe020d12e4ad635737468794313ff37d
21.0 MB Download
Sporosarcina.tar
md5:b184296365f25f7fa88ff1732f8f8261
70.4 MB Download
Sulfitobacter.tar
md5:efd6b78ddcd9d700a338452a4f3c3dc4
114.7 MB Download
Thalassospira.tar
md5:3d3ad4770ffc17aaeed9ea083757920d
84.6 MB Download
Thermococcus.tar
md5:15abd9ed33cba0776ea1843d92527fb0
66.2 MB Download
Thermus.tar
md5:0b0a6a4b55146e1a46b315107ebdf237
43.9 MB Download
Thioalkalivibrio.tar
md5:703fd1fcbdff635760cdfe94ee5e1fa1
73.3 MB Download
Treponema.tar
md5:d09ffc8d8452d60fe4635d1f59c4f3af
56.8 MB Download
Variovorax.tar
md5:bc535b0f078d51f0e57a066d4101c888
222.6 MB Download
Veillonella.tar
md5:c5de0128d9f19c5cae793228d8b278ef
27.2 MB Download
Virgibacillus.tar
md5:ffac4513cfe75d045645b82aa5081c92
63.2 MB Download
Weissella.tar
md5:4a42d5ddbb881af738b2e4f2519c4123
22.8 MB Download
Xenorhabdus.tar
md5:a32d2e951f4b2ffaa1bc8a24a52ea234
111.2 MB Download
81
166
views
downloads
All versions This version
Views 8176
Downloads 16697
Data volume 23.8 GB14.8 GB
Unique views 6461
Unique downloads 108

Share

Cite as