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" The data set consists of the following sub-directories: 1) "APSE_conserved_proteins_alns": Single-copy conserved genes codon sequences and alignments in FASTA format. 2) "APSE_phylogeny": Files used for APSE phylogenetic and recombination analyses. 3) "APSE_reannotations": 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*** 4) "APSE_toxin_lyzozyme": Files used for APSE toxin-cassette and lyzozyme-related gene phylogenies. 5) "Arsenophonus_PHASTER": PHASTER phage annotation output files organised by organisim and contig/scaffold. 6) "Hamiltonella_drafts": Newly-sequenced low-coverage draft Hamiltonella genomes in FASTA format. 7) "Hamiltonella_phylogeny": files used for Hamiltonella phylogenetic analysis. See enclosed README.txt file for more details.

Agence Nationale pour la Recherche (FR) [ANR-10-INBS-09]