Seance: reference-based phylogenetic analysis for 18S rRNA studies.

ABSTRACT:

Background

Marker gene studies often use short amplicons spanning one or more hypervariable regions from an rRNA gene to interrogate the community structure of uncultured environmental samples. Target regions are chosen for their discriminatory power, but the limited phylogenetic signal of short high-throughput sequencing reads precludes accurate phylogenetic analysis. This is particularly unfortunate in the study of microscopic eukaryotes where horizontal gene flow is limited and the rRNA gene is expected to accurately reflect the species phylogeny. A promising alternative to full phylogenetic analysis is phylogenetic placement, where a reference phylogeny is inferred using the complete marker gene and iteratively extended with the short sequences from a metagenetic sample under s

SUBMITTER: Medlar A 

PROVIDER: S-EPMC4265393 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature