Dataset Open Access

Model trees and associated simulated nucleotide sequences for testing phylogenetic inference methods

Alexis Criscuolo

This repository contains 142 tar.gz archive files, each containing nucleotide sequence data that have been simulated using INDELible for testing alignment-free phylogenetic inference methods. These datasets were generated by using the results (trees and model parameters) of 142 phylogenomic analyses of real-case data as model (available here). Initial sequence length was 5 Mbs, and an indel rate of 0.01 was set with indel length drawn from [1, 50000] according to a Zipf distribution with parameter 1.5 (see INDELible manual).

Each archive contains the following files/directories:

  • GTR.params.trees.tsv     a tab-delimited file summarizing the real-case GTR+Γ model parameters and the phylogenetic tree used to simulate the sequence dataset (gathered from https://zenodo.org/record/4034261)
  • tax.tsv                  a tab-delimited file containing the initial (col 1) and simplified (col 2) taxon names
  • model.nwk                a Newick-formatted file containing the initial model tree (gathered from GTR.params.trees.tsv) with simplified leaf names (following tax.tsv)
  • control.txt              the INDELible input file used to simulate the evolution of a sequence along the tree in model.nwk
  • seq/                     a directory containing the simulated sequences (one FASTA file per leaf in the tree in model.nwk)

___

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 (6.7 GB)
Name Size
dataset.001.tar.gz
md5:87ddbe2379e1cf28c6db1ca93b5afb20
39.1 MB Download
dataset.002.tar.gz
md5:f0470542ec2a46a225704421c459a539
40.3 MB Download
dataset.003.tar.gz
md5:2eb9b0dbd52b545f0be25da6f813e14a
56.3 MB Download
dataset.004.tar.gz
md5:a0a03a7757a89ea888f220e912067eda
33.3 MB Download
dataset.005.tar.gz
md5:f2fc85409ff408725c36bec6e42c2b4f
24.6 MB Download
dataset.006.tar.gz
md5:da1a7ebfcb0a9c9cb60d9f9fe54de5ca
50.8 MB Download
dataset.007.tar.gz
md5:43cb4b82485eaf840e25f411b4c7441a
50.4 MB Download
dataset.008.tar.gz
md5:6b34cb8f652f7e7eba3a41140a8d52a1
21.9 MB Download
dataset.009.tar.gz
md5:c0822897f0c041041378a3383d38df15
25.6 MB Download
dataset.010.tar.gz
md5:dd45417c3670b9d873143a39985d9b8e
34.3 MB Download
dataset.011.tar.gz
md5:f07969a9d96a292a32fbba6e28c81d6c
68.1 MB Download
dataset.012.tar.gz
md5:0b98bae9a6c4fe82e8bdde97b46d994d
31.0 MB Download
dataset.013.tar.gz
md5:6f13e58ee4be50c00dcc17ef2c4dd844
19.0 MB Download
dataset.014.tar.gz
md5:2d46650270e407340a1da88171158a2b
39.0 MB Download
dataset.015.tar.gz
md5:eafac1e5c29eff34b955c934db191a11
214.2 MB Download
dataset.016.tar.gz
md5:4b6f87f994233af644ee1e0f59492ec7
29.5 MB Download
dataset.017.tar.gz
md5:04c055bdaf60a1472de268c190968133
56.5 MB Download
dataset.018.tar.gz
md5:6521f94f669bb3c7c256214e3a2518e3
31.9 MB Download
dataset.019.tar.gz
md5:e9096da4221e696a39e9e055124a97cc
15.7 MB Download
dataset.020.tar.gz
md5:f5aff9f55a15714fe14ecd10c3bbad69
135.9 MB Download
dataset.021.tar.gz
md5:531f9c72ceb16980a6e8e5759e093a7a
29.9 MB Download
dataset.022.tar.gz
md5:e70d18770245d4747a56924be142ad4c
30.3 MB Download
dataset.023.tar.gz
md5:861336f08f2361e968b1c7a7e8be9029
36.6 MB Download
dataset.024.tar.gz
md5:89611995dc2a8d964eb777c8600f7f24
57.1 MB Download
dataset.025.tar.gz
md5:bb536d41f2ce8797bfe1539393848705
42.4 MB Download
dataset.026.tar.gz
md5:0fe1a1799658150a4e45b3fcf6e7b094
23.7 MB Download
dataset.027.tar.gz
md5:f032e43dc3a5ed34d6850147934a13b7
20.9 MB Download
dataset.028.tar.gz
md5:6ce9b45defac1c8bfcddafde3e0014fa
42.0 MB Download
dataset.029.tar.gz
md5:5012bf268b71fefbd2d8d73eb6a3f48a
44.2 MB Download
dataset.030.tar.gz
md5:672add39c449194aecd0972defb10475
18.7 MB Download
dataset.031.tar.gz
md5:9a3e539ec167491932b60624473de764
139.4 MB Download
dataset.032.tar.gz
md5:05e7f756b793e486d246f719031cd55e
27.4 MB Download
dataset.033.tar.gz
md5:e802d70036815782b0fba20826f4e511
16.3 MB Download
dataset.034.tar.gz
md5:51670c121a01027c55b3d528da28f6b0
29.5 MB Download
dataset.035.tar.gz
md5:16f15c73667f2f04f15112d270b79e99
22.5 MB Download
dataset.036.tar.gz
md5:ce46015444712939b337c76e1370551c
31.7 MB Download
dataset.037.tar.gz
md5:92be35ba5592aa2d9f70fd693dad4e5e
46.8 MB Download
dataset.038.tar.gz
md5:1f48e1bb5ad944420de99b61d11526ba
43.6 MB Download
dataset.039.tar.gz
md5:c9816db3c180aa5656b0258610670cc6
54.6 MB Download
dataset.040.tar.gz
md5:9bf8f88ec8d13957ea3a23e1fda84308
63.8 MB Download
dataset.041.tar.gz
md5:a91908679dce022b372a581d72aad562
39.3 MB Download
dataset.042.tar.gz
md5:986c2e3d7c221ccaab5b77820bc61bab
14.9 MB Download
dataset.043.tar.gz
md5:4014af3b383315cb4d00b2e512cb5d95
21.4 MB Download
dataset.044.tar.gz
md5:5e0aba9610847e319f8519231e2e6241
34.8 MB Download
dataset.045.tar.gz
md5:50ffb89ad1d8b0eda4a1207ebb5dce68
26.5 MB Download
dataset.046.tar.gz
md5:ef4181b98eadb063cc9d63ced5617b6c
43.9 MB Download
dataset.047.tar.gz
md5:83bd18d1db7fc1b5305abe94fe0e8c98
69.3 MB Download
dataset.048.tar.gz
md5:c9177bd630476188617dddc20012c2b3
30.0 MB Download
dataset.049.tar.gz
md5:8c177daf9c5e8b6dac7d3264789bea4c
15.0 MB Download
dataset.050.tar.gz
md5:4d267aacc3c734704898cf29954f621c
29.2 MB Download
dataset.051.tar.gz
md5:5b98cd3b768fa389fb9c14cc1aae8cd7
224.0 MB Download
dataset.052.tar.gz
md5:188375d100adcff2f93e2bb18534ba72
20.5 MB Download
dataset.053.tar.gz
md5:fc0545221f67024b7344a0a860a68e5f
28.0 MB Download
dataset.054.tar.gz
md5:f5d346d935061026799ea7e644091d9f
33.4 MB Download
dataset.055.tar.gz
md5:a5d287fd6ea03712dec6bb334c08ddda
16.4 MB Download
dataset.056.tar.gz
md5:11df4df9e27b5b76a02f59c5daf4448f
20.3 MB Download
dataset.057.tar.gz
md5:58baee7d3eed971ec26815c3cfa17153
32.2 MB Download
dataset.058.tar.gz
md5:47fa1e35fbe7dd23a75402830f6524b1
15.6 MB Download
dataset.059.tar.gz
md5:9af49d2c701550e90bfc41c1fa7e596c
48.2 MB Download
dataset.060.tar.gz
md5:2d87f2c10d92cf7847a6a68fa3ed6bdc
16.8 MB Download
dataset.061.tar.gz
md5:43ab64118e7572d8a02a17536b00ecdd
125.4 MB Download
dataset.062.tar.gz
md5:f01a3f25a41102c8fc0a91170483fe1f
40.5 MB Download
dataset.063.tar.gz
md5:52003bac85f929b90629879405968128
28.4 MB Download
dataset.064.tar.gz
md5:25eb60cda84453a30b29f539ca291194
51.7 MB Download
dataset.065.tar.gz
md5:932655ffc26be696790e1691a67734ea
38.1 MB Download
dataset.066.tar.gz
md5:fe0406bb9c9c34a40b056acfc1702310
24.4 MB Download
dataset.067.tar.gz
md5:0fb05ffe29fb7c6c1491b84ec0f7f33a
23.1 MB Download
dataset.068.tar.gz
md5:9d40273fdfa9a0ed6fe783b1292180df
25.1 MB Download
dataset.069.tar.gz
md5:a479cca796be1e0dbea5b805b9541b4b
31.9 MB Download
dataset.070.tar.gz
md5:a84df25017a20d64baafa420cf869e6e
15.5 MB Download
dataset.071.tar.gz
md5:6789e3b977ae18c32051fe787bb8deab
38.4 MB Download
dataset.072.tar.gz
md5:ae882627631c7a86f2d21d019a8faa8d
48.3 MB Download
dataset.073.tar.gz
md5:17defce8a377d330cd585f8faf4ee3c5
42.4 MB Download
dataset.074.tar.gz
md5:82397229f1a99d830dbd7acf894c072a
79.4 MB Download
dataset.075.tar.gz
md5:227f40849c15c16e9112fc6b25dfb1e6
33.8 MB Download
dataset.076.tar.gz
md5:a0392fccbb1b7f35d9ead6c364c74e41
47.5 MB Download
dataset.077.tar.gz
md5:84b21dd9d4ad4bb5c2edce1df198a51e
21.0 MB Download
dataset.078.tar.gz
md5:6edf165a626210cffbd7c461b38e8777
98.2 MB Download
dataset.079.tar.gz
md5:a8eeac8979430ee49cfce39cb03ab126
26.6 MB Download
dataset.080.tar.gz
md5:ab3f495f40e0a961bdaae8f51ef634ed
21.8 MB Download
dataset.081.tar.gz
md5:0bfb5b65583bf62f221f2340df7e2f79
73.5 MB Download
dataset.082.tar.gz
md5:e85141c353a7a23cd56662a8f5e88cd4
178.4 MB Download
dataset.083.tar.gz
md5:6970970f8870b941594d886cfba6442b
91.1 MB Download
dataset.084.tar.gz
md5:c47c29b207e812c7b63f85abd25ee031
32.5 MB Download
dataset.085.tar.gz
md5:a2e027cfdebdd2a0120515ed97316a3e
48.9 MB Download
dataset.086.tar.gz
md5:a4e3f5dc27ba2115d2ae89261023ef35
108.5 MB Download
dataset.087.tar.gz
md5:7cfbdea2a9be370968a82afe57798783
38.7 MB Download
dataset.088.tar.gz
md5:bb063071743bad0755cbfb9d19734337
133.1 MB Download
dataset.089.tar.gz
md5:1df5c043d9f5e0776101a8d74441102e
69.6 MB Download
dataset.090.tar.gz
md5:8913b5f2a38d97ab83dd4ed0b0acc94d
41.2 MB Download
dataset.091.tar.gz
md5:fd865bcf198684b64c81a499c127393b
67.6 MB Download
dataset.092.tar.gz
md5:75af52373f9f515823a68d5d190653ac
25.6 MB Download
dataset.093.tar.gz
md5:a71fd11744b1a59167711c176cb34b04
31.7 MB Download
dataset.094.tar.gz
md5:9e9cfe7d2935165146e9854a62a1129f
18.7 MB Download
dataset.095.tar.gz
md5:196d6fffe17fc5b5bcfbb70bcf6cab9f
51.5 MB Download
dataset.096.tar.gz
md5:cc0bb44139bccc65183ee1b986e0e9dc
27.1 MB Download
dataset.097.tar.gz
md5:f182696a375a9daed5646f91c9748826
107.3 MB Download
dataset.098.tar.gz
md5:12579f5278a48cd6540dd5e44464df04
72.0 MB Download
dataset.099.tar.gz
md5:92bfcde44b7c84f64022079fdc8e2807
18.2 MB Download
dataset.100.tar.gz
md5:03e532ddbf49c345417cbd4378fc58f5
15.4 MB Download
dataset.101.tar.gz
md5:05aaed53904f2e08307ee765baf28e72
105.9 MB Download
dataset.102.tar.gz
md5:81945458641047c7dcc1f82eb6f13b88
36.8 MB Download
dataset.103.tar.gz
md5:eabc52a2e6588c1f17c96644c2e02160
16.4 MB Download
dataset.104.tar.gz
md5:bb34574e42bff97d3bf01114c0660229
47.7 MB Download
dataset.105.tar.gz
md5:378f14473ccc17adafc0f5ca68c181f2
15.0 MB Download
dataset.106.tar.gz
md5:af89fd530baf23a9ceb41f4ef16ed979
45.3 MB Download
dataset.107.tar.gz
md5:8075d920efb7889282cc251b7cb28278
34.6 MB Download
dataset.108.tar.gz
md5:f0b57472f0e7c99ad6643dac7e970dd1
88.3 MB Download
dataset.109.tar.gz
md5:69fd3ec03498a109865b45ae19854516
57.4 MB Download
dataset.110.tar.gz
md5:57c30bf0e5c5b37683e81d07aa8b08ec
17.0 MB Download
dataset.111.tar.gz
md5:3d1ae059c44d291502d07fdc83001614
15.9 MB Download
dataset.112.tar.gz
md5:667c3072526b31ac094d2827f028d100
17.8 MB Download
dataset.113.tar.gz
md5:7f4720a19573a19ba53415efe1a5a45c
59.6 MB Download
dataset.114.tar.gz
md5:47eac79d20de9b20b4cc4defd0ecf755
26.6 MB Download
dataset.115.tar.gz
md5:6d2b0b06473f0569842a5694c4b6869f
44.2 MB Download
dataset.116.tar.gz
md5:e0b542eb9baac817d63cde053efe90fc
20.3 MB Download
dataset.117.tar.gz
md5:2006714223a98ade746dfffdc536a4cb
208.4 MB Download
dataset.118.tar.gz
md5:4e1004ad9ef3fb494bf1828d58d5029e
27.4 MB Download
dataset.119.tar.gz
md5:fa8ccceeb57c2ae61dbcbeda95628324
18.9 MB Download
dataset.120.tar.gz
md5:5bb7814987268263d18a1964407670bd
39.9 MB Download
dataset.121.tar.gz
md5:c907c77b775a5cae524e94b7f0f79625
41.0 MB Download
dataset.122.tar.gz
md5:b4e53be50539e4c1fb92ef33f36dc9b5
66.8 MB Download
dataset.123.tar.gz
md5:cb716ebedc7683917339fcc4c65b1086
36.3 MB Download
dataset.124.tar.gz
md5:1c2366d26bc99af75249b2139a548200
76.0 MB Download
dataset.125.tar.gz
md5:36727757bcf58b5b76bd675791b762d2
23.2 MB Download
dataset.126.tar.gz
md5:f3a9ee523a013d79f982fb8d6516ef73
45.5 MB Download
dataset.127.tar.gz
md5:8fce6f24c59603d931460f632fba601b
61.5 MB Download
dataset.128.tar.gz
md5:5c9028ab28ecd4dbb3a56ff8cd76e3a6
213.2 MB Download
dataset.129.tar.gz
md5:d93eba0102f56fe378e50c3cff669f6a
49.8 MB Download
dataset.130.tar.gz
md5:e8ee212b3ea75b3eb449d66c4b43fa70
34.1 MB Download
dataset.131.tar.gz
md5:dda05e59c6581e296ccc478c7ce88ade
29.2 MB Download
dataset.132.tar.gz
md5:f58a5a88e9c1096ed514c0cf0e249926
41.5 MB Download
dataset.133.tar.gz
md5:c507d516923bbcb0315587f3ce946887
24.1 MB Download
dataset.134.tar.gz
md5:bc63606353eda07a4b97d9bbc5254991
47.4 MB Download
dataset.135.tar.gz
md5:17e81c8bf492db3023e36a0eba9ca3a3
25.3 MB Download
dataset.136.tar.gz
md5:916726cfbdc335ab4c2b111955db367c
37.3 MB Download
dataset.137.tar.gz
md5:38fe37ec0713df152c82dbcc57ea3d37
52.1 MB Download
dataset.138.tar.gz
md5:1fc63cc3c554c1e9b51c421585d628c8
47.7 MB Download
dataset.139.tar.gz
md5:ede341287de834b50a28d889b1b11d6d
18.9 MB Download
dataset.140.tar.gz
md5:584c12a43e8c6392f6003cf2a759a678
29.5 MB Download
dataset.141.tar.gz
md5:57388f478d61a8b557ad2804079a7952
23.8 MB Download
dataset.142.tar.gz
md5:00a2c81ad693f70dbbbe4c09b2e1296e
39.2 MB Download
53
338
views
downloads
All versions This version
Views 5353
Downloads 338338
Data volume 14.8 GB14.8 GB
Unique views 4343
Unique downloads 66

Share

Cite as