MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation.

ABSTRACT:

Background

The nonparametric bootstrap is widely used to measure the branch support of phylogenetic trees. However, bootstrapping is computationally expensive and remains a bottleneck in phylogenetic analyses. Recently, an ultrafast bootstrap approximation (UFBoot) approach was proposed for maximum likelihood analyses. However, such an approach is still missing for maximum parsimony.

Results

To close this gap we present MPBoot, an adaptation and extension of UFBoot to compute branch supports under the maximum parsimony principle. MPBoot works for both uniform and non-uniform cost matrices. Our analyses on biological DNA and protein showed that under uniform cost matrices, MPBoot runs on average 4.7 (DNA) to 7 times (protein data) (range: 1.2-20.7) faster than the standard pa

SUBMITTER: Hoang DT 

PROVIDER: S-EPMC5796505 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature