Dataset Open Access

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

Alexis Criscuolo


DCAT Export

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    <dct:title>Model trees and associated simulated nucleotide sequences for testing phylogenetic inference methods</dct:title>
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    <dct:description>&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;</dct:description>
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