Supplementary Files for Kawato et al. (2023) "Evolutionary genomics of white spot syndrome virus"

Online_Resource_1_MAGs.zip: Draft metagenome-assembled genomes (MAGs) of WSSV identified from publicly available high-throughput sequencing datasets. Available in FASTA (.fa) and DDBJ (.ddbj) formats. Online_Resource_2_whole_genome_alignments.zip: clean.full.aln: FASTA-format multiple sequence alignment of 61 WSSV genomesclean2.full.aln: FASTA-format multiple sequence alignment of 48 WSSV genomesclean3.full.aln: FASTA-format multiple sequence alignment of 40 WSSV genomesclean.full.aln.treefile: Newick-format maximium-likelihood phylogenetic tree generated from clean.full.alnclean2.full.aln.treefile: Newick-format maximium-likelihood phylogenetic tree generated from clean2.full.alnclean3.full.aln.treefile: Newick-format maximium-likelihood phylogenetic tree generated from clean3.full.alnOnline_Resource_3_BEAST_trees.zip: BEAST2 XML files (.xml) and Nexus-format phylogenetic trees (.nex) for Bayesian divergence time esimation assuming different population dynamics (coalescent constant, coalescent exponential, and coalscent Bayesian skyline) and substitution models (HKY and GTR) Online_Resource_4_subgenomic_alignments.zip: subegenomic alignments used in the recombination analyses. Online_Resource_5_genomic_deletions.zip: multiple sequence alignments of genomic deletions. 2023-09-10: Missing file (ORF14-15.fa) in Online_Resource_5_genomic_deletions.zip has been added.