Co-phylog: an assembly-free phylogenomic approach for closely related organisms.

ABSTRACT: With the advent of high-throughput sequencing technologies, the rapid generation and accumulation of large amounts of sequencing data pose an insurmountable demand for efficient algorithms for constructing whole-genome phylogenies. The existing phylogenomic methods all use assembled sequences, which are often not available owing to the difficulty of assembling short-reads; this obstructs phylogenetic investigations on species without a reference genome. In this report, we present co-phylog, an assembly-free phylogenomic approach that creates a 'micro-alignment' at each 'object' in the sequence using the 'context' of the object and calculates pairwise distances before reconstructing the phylogenetic tree based on those distances. We explored the parameters' usages and the optimal working ra

SUBMITTER: Yi H 

PROVIDER: S-EPMC3627563 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature