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:

accn.tax.tsv           a tab-delimited file containing the assembly accession (col 1) and an associated taxon name (col 2) for each selected genome (one per line)

gff/                   a directory containing a gzip-compressed GFF3 file (as returned by the annotation tool Prokka) for each genome specified in accn.tax.tsv

cds.fna.gz             a gzip-compressed FASTA file containing all the coding sequences (at the codon level) from the GFF3 files in the directory gff/

msa/                   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 Roary from the GFF3 files in gff/)

supermatrix.fasta.gz   a gzip-compressed FASTA file obtained by concatenating all the multiple codon sequence alignments in the directory msa/

tree.nwk               a Newick-formatted file containing a maximum-likelihood (ML) phylogenetic tree inferred from the file supermatrix.fasta.gz using IQ-TREE

iqtree.txt             a txt file summarizing the ML estimates of the GTR+Γ evolutionary model parameters, as returned by IQ-TREE when inferring the phylogenetic tree tree.nwk

A summary of the 142 phylogenomic analyses can be found in the tab-delimited file GTR.params.tree.tsv. Each line corresponds to one genus and contains the 12 following fields:
  [1]     genus name,
  [2-5]   frequencies of T, C, A, G, respectively,
  [6-10]  C-T, A-T, G-T, A-C, C-G rate parameters, respectively (normalized such that A-G rate = 1),
  [11]    Γ shape parameter alpha,
  [12]    Newick-formatted phylogenetic tree.

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Criscuolo A (2020) On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference. (submitted)