AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.

ABSTRACT: A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automa

SUBMITTER: Zhou C 

PROVIDER: S-EPMC4044049 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature