Homology-Aware Phylogenomics at Gigabase Scales.

ABSTRACT: Obstacles to inferring species trees from whole genome data sets range from algorithmic and data management challenges to the wholesale discordance in evolutionary history found in different parts of a genome. Recent work that builds trees directly from genomes by parsing them into sets of small $k$-mer strings holds promise to streamline and simplify these efforts, but existing approaches do not account well for gene tree discordance. We describe a "seed and extend" protocol that finds nearly exact matching sets of orthologous $k$-mers and extends them to construct data sets that can properly account for genomic heterogeneity. Exploiting an efficient suffix array data structure, sets of whole genomes can be parsed and converted into phylogenetic data matrices rapidly, with contiguous bloc

SUBMITTER: Sanderson MJ 

PROVIDER: S-EPMC5790135 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature