Phylogenomic analyses of 142 prokaryotic genera

This repository contains 142 tar archive files, each corresponding to a prokaryotic genus. Each archive contains the following files/directories: <code>accn.tax.tsv </code> a tab-delimited file containing the assembly accession (col 1) and an associated taxon name (col 2) for each selected genome (one per line) <code>gff/ </code> a directory containing a gzip-compressed GFF3 file (as returned by the annotation tool <em>Prokka</em>) for each genome specified in <code>accn.tax.tsv</code> <code>cds.fna.gz </code> a gzip-compressed FASTA file containing all the coding sequences (at the codon level) from the GFF3 files in the directory <code>gff/</code> <code>msa/ </code> a directory containing multiple amino acid and codon sequence alignments (compressed FASTA files with extensions .afa.gz and .afc.gz, respectively) for each cluster of at least four homologous sequences (as determined by the pipeline <em>Roary</em> from the GFF3 files in <code>gff/</code>) <code>supermatrix.fasta.gz </code> a gzip-compressed FASTA file obtained by concatenating all the multiple codon sequence alignments in the directory <code>msa/</code> <code>tree.nwk </code> a Newick-formatted file containing a maximum-likelihood (ML) phylogenetic tree inferred from the file <code>supermatrix.fasta.gz</code> using <em>IQ-TREE</em> <code>iqtree.txt </code> a txt file summarizing the ML estimates of the GTR+Γ evolutionary model parameters, as returned by <em>IQ-TREE</em> when inferring the phylogenetic tree <code>tree.nwk</code> A summary of the 142 phylogenomic analyses can be found in the tab-delimited file <code>GTR.params.tree.tsv</code>. Each line corresponds to one genus and contains the 12 following fields:<br> <code>[1] </code> genus name,<br> <code>[2-5] </code> frequencies of T, C, A, G, respectively,<br> <code>[6-10]</code> C-T, A-T, G-T, A-C, C-G rate parameters, respectively (normalized such that A-G rate = 1),<br> <code>[11] </code> Γ shape parameter alpha,<br> <code>[12] </code> Newick-formatted phylogenetic tree. _____ 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