Accurate and efficient reconstruction of deep phylogenies from structured RNAs.

ABSTRACT: Ribosomal RNA (rRNA) genes are probably the most frequently used data source in phylogenetic reconstruction. Individual columns of rRNA alignments are not independent as a consequence of their highly conserved secondary structures. Unless explicitly taken into account, these correlation can distort the phylogenetic signal and/or lead to gross overestimates of tree stability. Maximum likelihood and Bayesian approaches are of course amenable to using RNA-specific substitution models that treat conserved base pairs appropriately, but require accurate secondary structure models as input. So far, however, no accurate and easy-to-use tool has been available for computing structure-aware alignments and consensus structures that can deal with the large rRNAs. The RNAsalsa approach is designed to f

SUBMITTER: Stocsits RR 

PROVIDER: S-EPMC2764418 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature