Dataset Open Access

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

Alexis Criscuolo


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    <subfield code="u">https://zenodo.org/record/4034644/files/dataset.142.tar.gz</subfield>
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    <subfield code="c">2020-09-17</subfield>
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  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="u">Institut Pasteur</subfield>
    <subfield code="0">(orcid)0000-0002-8212-5215</subfield>
    <subfield code="a">Alexis Criscuolo</subfield>
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    <subfield code="a">Model trees and associated simulated nucleotide sequences for testing phylogenetic inference methods</subfield>
  </datafield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="u">https://creativecommons.org/licenses/by/4.0/legalcode</subfield>
    <subfield code="a">Creative Commons Attribution 4.0 International</subfield>
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    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
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  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&lt;p&gt;This repository contains 142 tar.gz archive files, each containing nucleotide sequence data that have been simulated using &lt;a href="http://abacus.gene.ucl.ac.uk/software/indelible/"&gt;&lt;em&gt;INDELible&lt;/em&gt;&lt;/a&gt; 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 &lt;a href="https://zenodo.org/record/4034261"&gt;here&lt;/a&gt;). 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 &lt;em&gt;INDELible&lt;/em&gt; &lt;a href="http://abacus.gene.ucl.ac.uk/software/indelible/manual/model.shtml"&gt;manual&lt;/a&gt;).&lt;/p&gt;

&lt;p&gt;Each archive contains the following files/directories:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;&lt;code&gt;GTR.params.trees.tsv &amp;nbsp; &lt;/code&gt; &amp;nbsp; a tab-delimited file summarizing the real-case GTR+&amp;Gamma; model parameters and the phylogenetic tree used to simulate the sequence dataset (gathered from &lt;a href="https://zenodo.org/record/4034261"&gt;https://zenodo.org/record/4034261&lt;/a&gt;)&lt;/li&gt;
	&lt;li&gt;&lt;code&gt;tax.tsv &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp;&amp;nbsp; &lt;/code&gt; &amp;nbsp; a tab-delimited file containing the initial (col 1) and simplified (col 2) taxon names&lt;/li&gt;
	&lt;li&gt;&lt;code&gt;model.nwk &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp;&amp;nbsp; &lt;/code&gt; &amp;nbsp; a &lt;a href="https://evolution.genetics.washington.edu/phylip/newicktree.html"&gt;Newick&lt;/a&gt;-formatted file containing the initial model tree (gathered from &lt;code&gt;GTR.params.trees.tsv&lt;/code&gt;) with simplified leaf names (following &lt;code&gt;tax.tsv&lt;/code&gt;)&lt;/li&gt;
	&lt;li&gt;&lt;code&gt;control.txt &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp;&amp;nbsp; &lt;/code&gt; &amp;nbsp; the &lt;em&gt;INDELible&lt;/em&gt; input file used to simulate the evolution of a sequence along the tree in &lt;code&gt;model.nwk&lt;/code&gt;&lt;/li&gt;
	&lt;li&gt;&lt;code&gt;seq/ &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &lt;/code&gt; &amp;nbsp; a directory containing the simulated sequences (one FASTA file per leaf in the tree in &lt;code&gt;model.nwk&lt;/code&gt;)&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;___&lt;/p&gt;

&lt;p&gt;Criscuolo A (2020) &lt;em&gt;On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference&lt;/em&gt;. F1000Research, 9:1309. &lt;a href="https://doi.org/10.12688/f1000research.26930.1"&gt;doi:10.12688/f1000research.26930.1&lt;/a&gt;&lt;/p&gt;</subfield>
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    <subfield code="a">10.5281/zenodo.4034643</subfield>
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    <subfield code="a">10.5281/zenodo.4034644</subfield>
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  </datafield>
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    <subfield code="a">dataset</subfield>
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