MPboot

MPBOOT

MPBOOT is an efficient open-source program to reconstruct maximum parsimony phylogenetic trees for large DNA and protein sequence alignments. Importantly, MPBoot provides a fast approximation for maximum parsimony bootstrap, inspired by a similar methodology that is used for maximum likelihood. (Minh et al., 2013)

Code/manual here.

User support group is here.

Input files:MPBOOT accepts as input a matrix in phylip/relaxed phylip format.

Output files:

The table below shows the kinds of results returned by CIPRES Science Gateway:

Input File Names Sample File from a Test (large file)
input file (phylip format) mpboot.phy
tree file (phylip/Newick format) treefile.tre
Output File Types File Name
MPBoot report file: example.phy.mpboot mpboot.mpboot
Maximum-parsimony tree file: example.phy.treefile mpboot.treefile
Split support values file: example.phy.splits.nex mpboot.splits.nex
Consensus tree file: example.phy.contree mpboot.contree
Screen log file: example.phy.log mpboot.log

 

If you use MPBOOT here, please cite:

D.T. Hoang, L.S. Vinh, T. Flouri, A. Stamatakis, A. von Haeseler, and B.Q. Minh (2018) MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol. Biol., 18, 11. MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol. Biol., 18, 11..

If there is a tool or a feature you need, please let us know.

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