Dataset Open Access

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

Alexis Criscuolo


DataCite XML Export

<?xml version='1.0' encoding='utf-8'?>
<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.1/metadata.xsd">
  <identifier identifierType="DOI">10.5281/zenodo.4034644</identifier>
  <creators>
    <creator>
      <creatorName>Alexis Criscuolo</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-8212-5215</nameIdentifier>
      <affiliation>Institut Pasteur</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Model trees and associated simulated nucleotide sequences for testing phylogenetic inference methods</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>phylogenetics</subject>
    <subject>simulation</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-09-17</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4034644</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4034643</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&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;</description>
  </descriptions>
</resource>
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