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

This repository contains 142 tar.gz archive files, each containing nucleotide sequence data that have been simulated using <em>INDELible</em> 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 <em>INDELible</em> manual). Each archive contains the following files/directories: <code>GTR.params.trees.tsv </code> 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) <code>tax.tsv </code> a tab-delimited file containing the initial (col 1) and simplified (col 2) taxon names <code>model.nwk </code> a Newick-formatted file containing the initial model tree (gathered from <code>GTR.params.trees.tsv</code>) with simplified leaf names (following <code>tax.tsv</code>) <code>control.txt </code> the <em>INDELible</em> input file used to simulate the evolution of a sequence along the tree in <code>model.nwk</code> <code>seq/ </code> a directory containing the simulated sequences (one FASTA file per leaf in the tree in <code>model.nwk</code>) ___ Criscuolo A (2020) <em>On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference</em>. F1000Research, 9:1309. doi:10.12688/f1000research.26930.1