Jan 1, 2018 | By: Admin
MPBoot is an open-source and efficient 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 for maximum likelihood (Minh et al., 2013). If you use MPBoot in a paper 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. https://doi.org/10.1186/s12862-018-1131-3
For feedback or bug reports please post a question to the IQ-TREE forum:
Precomplied executables are provided for computers with SSE4 or AVX support:
tar xvzf mpboot-avx-1.1.0-Linux.tar.gzunder Unix). This should create a directory
binfolder inside the extracted folder. You can rename it to
mpbootand copy to your system search path such that you can invoke it by entering
mpbootfrom the terminal.
In case you cannot find executables for your platforms or want to compile the source code:
buildin the uncompressed source code folder:
cmake .. -DIQTREE_FLAGS=sse4 -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++
avxin above command if you decide to run MPBoot on AVX-supported machines.
mpboot-avx) once the make command is done.
mpboot with actual path to executable)
Reconstruct maximum parsimony tree from a sequence alignment (
mpboot -s example.phy
Reconstruct MP tree and assess branch supports with the MPBoot method (1000 replicates):
mpboot -s example.phy -bb 1000
Display all usage options:
Input alignment file
example.phy is in PHYLIP format. MPBoot also supports FASTA or NEXUS format.
|Option||Usage and meaning|
|-mulhits||Store multiple equally parsimonious trees per bootstrap replicate|
|-ratchet_iter ||Number of non-ratchet iterations before each ratchet iteration (default: 1)|
|-ratchet_wgt ||Weight to add to each site selected for perturbation during ratchet (default: 1)|
|-ratchet_percent ||Percentage of informative sites selected for perturbation during ratchet (default: 50)|
|-ratchet_off||Turn of ratchet, i.e. Only use tree perturbation|
|-spr_rad ||Maximum radius of SPR (default: 6)|
|-cand_cutoff <#s>||Use top #s percentile as cutoff for selecting bootstrap candidates (default: 10)|
|-opt_btree_off||Turn off refinement step on the final bootstrap tree set|
|-nni_pars||Hill-climb by NNI instead of SPR|
|-cost ||Read |
The code was originally derived from the IQ-TREE software and the Phylogenetic likelihood library.
D.T. Hoang and L.S. Vinh were financially supported by Vietnam National Foundation for Science and Technology Development (Grant #102.01-2013.04). B.Q. Minh and A. von Haeseler were supported by the Austrian Science Fund (FWF I-2805-B29), T. Flouri and A. Stamatakis by the German Science Foundation (DFG STA860-6/1), and the Klaus Tschira Foundation.