Jul 1, 2018 Release
This version contains a number of bugfixes and is highly recommended for all users.
-lmapoption (reported by Giap Nguyen).
-bsam) for standard bootstrap (
-b) and jackknife (
-m ...MERGE) (reported by Guoqing Li).
-t RANDOM(reported by Karen Meusemann).
May 8, 2018 Release
Apr 30, 2018 Release
--runsto perform multiple tree searches (issue #64 requested by David Maddison). This is motivated by a recent evaluation (Zhou et al. 2018) showing that 10 independent runs outperformed single run in terms of likelihood maximisation.
--show-lhto compute tree log-likelihood without parameter optimisation (issue #67).
+Pfor PoMo model string (thanks Carolin Kosiol).
GTR20(reported by Dominik Schrempf).
-alrt(reported by Guifre Torruella Cortes).
+ASCmodel when some states are rare (reported by Paul Madeira).
-zoption with rooted trees in the presence of identical sequences (reported by cjp1043).
Mar 22, 2018 Release
This version improves software stability and highly recommended to update for all users.
-t) and partition model (reported by Dieter Waechter).
-spoption (edge-unlinked) and
Too many iterations in tqlito WARNING.
-mtree(reported by Mark Miller).
-sppby temporarily turning on NNI5 instead of NNI1 (originally reported by Xiaofan).
-ntmaxoption to specify maximum number of threads by
-nt AUTOoption (requested by @sjspielman).
-j(requested by Emmanuel Toussaint).
-versionto display version number (requested by David Maddison).
Mar 1, 2018 Release
LG+C10or similar models (reported by Craig Herbold)
-netoption (reported by Cameron Weadick)
--write-branchesto write branch lengths of tree (and partition trees) into
.branches.csvfile (requested by Rob Lanfear)
-ooption to specify a comma-separated list of outgroup taxa (requested by Andrew Roger)
Jan 1, 2018 Publication
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.
Dec 29, 2017 Release
Dec 23, 2017 Release
This is the major update of the IQ-TREE software for phylogenomic reconstruction.
IMPORTANT: The checkpoint file is no more compatible with 1.5.X, 1.6.betaX or earlier versions. An error message will be printed if you try to recover the run from old versions. Sequential and multicore versions are merged, thus
iqtree-omp executable becomes
Notable new features:
.model.gzto save space.
-fastto match the speed of FastTree program while still obtaining better trees.
-bnnito further optimize UFBoot trees by nearest neighbor interchange (NNI) directly on corresponding bootstrap alignments (UFBoot2+NNI).
-asrfor ancestral sequence reconstruction written to
-rclusterfto perform fast relaxed clustering algorithm of PartitionFinder2.
-rcluster-maxto limit maximum number of partition pairs for merging with rcluster algorithm.
-alninfoto print alignment sites statistics to .alninfo file (requested by Federico Gaiti).
-czbto collapse zero branches, useful by bootstrapping with polytomy.
-wqloption now prints quartet area and corner in
.quartetlhfile (requested by Karen Meusemann).
-bspec GENE) and GENESITE resampling (
-bspec GENESITE) for standard bootstrap with partition models.
New features for PoMo models:
Dec 4, 2017 Release
This version improves software stability and contains bugfixes:
-msetoption works with binary and morphological models.
-ooption) does not appear in alignment.
Sep 26, 2017 Opinion
It is often hard to predict the significance and long-term impact of new innovations, but the introduction of ModelFinder (1), a novel model-selection method for accurate phylogenetic estimates, is likely to be on par with Yang’s ground-breaking discovery, in 1994, of a simple one-parameter Gamma model (2) of rate heterogeneity across sites, the first model-selection method (3) to be widely used in molecular phylogenetics, and the rise of Bayesian phylogenetic methods (4), (5).
Published in 1994, Yang’s one-parameter model has been used in most of the subsequent molecular phylogenetic research but its success has perhaps also led to his other discovery, in 1995, of a more versatile model (6) of rate heterogeneity across sites being overlooked. ModelFinder includes both models, and the first results show that the more flexible model often is needed to obtain accurate estimates of phylogenetic trees and evolutionary processes.
These results call into question much of the last two decades of phylogenetic research, which relied on phylogenetic methodology that ignored the more versatile model of rate heterogeneity across sites.
The advent of ModelFinder opens a new era of opportunities, where accurate phylogenetic estimates can be obtained and used to answer important biological questions, and where controversial as well as long-standing evolutionary hypotheses can be tested using novel ways of modelling sequence evolution.