AliGROOVE--visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support.

ABSTRACT:

Background

Masking of multiple sequence alignment blocks has become a powerful method to enhance the tree-likeness of the underlying data. However, existing masking approaches are insensitive to heterogeneous sequence divergence which can mislead tree reconstructions. We present AliGROOVE, a new method based on a sliding window and a Monte Carlo resampling approach, that visualizes heterogeneous sequence divergence or alignment ambiguity related to single taxa or subsets of taxa within a multiple sequence alignment and tags suspicious branches on a given tree.

Results

We used simulated multiple sequence alignments to show that the extent of alignment ambiguity in pairwise sequence comparison is correlated with the frequency of misplaced taxa in tree reconstructions. The appr

SUBMITTER: Kuck P 

PROVIDER: S-EPMC4167143 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature