Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

ABSTRACT:

Background

While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood) and studied ways to improve the accuracy of trees obtained from such datasets.

Results

We found that the pattern of gappiness in m

SUBMITTER: Hartmann S 

PROVIDER: S-EPMC2359737 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature