MPBoot: Fast phylogenetic maximum parsimony tree inference and bootstrap approximation
Center for Integrative Bioinformatics Vienna
Max F. Perutz Laboratories
Dr. Bohr Gasse 9
A-1030 Vienna, Austria
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   Max F. Perutz Laboratories
   University of Vienna
   Medical University, Vienna

   Deep Metazoan Phylogeny
   MaBS group
   Max Perutz Library

MPBoot: Fast phylogenetic maximum parsimony tree inference and bootstrap approximation

About MPBoot

MPBoot is an efficient program for parsimony analysis. The program can reconstruct maximum parsimony trees for large DNA and protein sequence alignments. More importantly, it implements the method MPBoot for approximating maximum parsimony bootstrap. The method was inspired by the ultrafast bootstrap approximation for maximum likelihood (UFBoot; Minh et al. 2013) and other local optimization techniques for tree search.


August 2017: Version 1.1.0 is released with two important features: (i) SPR moves for hill-climbing search and (ii) Capability to deal with a transition cost matrix between character states.
October 2015: We are pleased to announce version 1.0.0.


Please read carefully before using MPBoot the first time!

User Manual and Tutorial 1.1

Software and source code

MPBoot offers sequential versions on Linux:
Linux download

For Linux 64-bit:

Source code:

GitHub repository:

For the most up-to-date source code, please checkout the MPBoot repository. Note that, compiling code cloned from the GitHub has a few extra steps compared to compiling the source code from this website.


D.T.H and L.S.V were financially supported by Vietnam National Foundation for Science and Technology Development (Grant #102.01-2013.04). B.Q.M. and A.v.H were supported by the Austrian Science Fund (FWF I-2805-B29), T.F and A.S by the German Science Foundation (DFG STA860-6/1), and the Klaus Tschira Foundation.

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