An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data.

ABSTRACT:

Background

Next-generation sequencing technologies are rapidly generating whole-genome datasets for an increasing number of organisms. However, phylogenetic reconstruction of genomic data remains difficult because de novo assembly for non-model genomes and multi-genome alignment are challenging.

Results

To greatly simplify the analysis, we present an Assembly and Alignment-Free (AAF) method ( https://sourceforge.net/projects/aaf-phylogeny ) that constructs phylogenies directly from unassembled genome sequence data, bypassing both genome assembly and alignment. Using mathematical calculations, models of sequence evolution, and simulated sequencing of published genomes, we address both evolutionary and sampling issues caused by direct reconstruction, including homoplasy, seque

SUBMITTER: Fan H 

PROVIDER: S-EPMC4501066 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature