Supplementary phylogenetic data for Rouïl et. al. 2020 "The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals"

<p>Supplementary phylogenetic data for Rou&iuml;l <em>et. al.</em> 2020 &quot;The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals&quot;</p> <p>&nbsp;</p> <p>The data set consists of the following sub-directories:</p> <p>1) &quot;APSE_conserved_proteins_alns&quot;: Single-copy conserved genes codon sequences and alignments in FASTA format.</p> <p>2) &quot;APSE_phylogeny&quot;: Files used for APSE phylogenetic and recombination analyses.</p> <p>3) &quot;APSE_reannotations&quot;: GenBank-formatted files of the assemblies and re-annotations of APSE phages. Newly-sequenced phages deposited at the European nucleotide Archive are also included. ***New in this version***</p> <p>4) &quot;APSE_toxin_lyzozyme&quot;: Files used for APSE toxin-cassette and lyzozyme-related gene phylogenies.</p> <p>5) &quot;Arsenophonus_PHASTER&quot;: PHASTER phage annotation output files organised by organisim and contig/scaffold.</p> <p>6) &quot;Hamiltonella_drafts&quot;:&nbsp;Newly-sequenced low-coverage draft <em>Hamiltonella</em> genomes in FASTA format.</p> <p>7) &quot;Hamiltonella_phylogeny&quot;:&nbsp;files used for <em>Hamiltonella</em> phylogenetic analysis.</p> <p>&nbsp;</p> <p>See enclosed README.txt file for more details.</p> <p>&nbsp;</p> <p>* ver. 1.1.1: Updated annotations for APSE genomes including inteins missing in previous annotation files.</p>