Aug 12, 2016 Announcement
We have released an IQ-TREE variant which implements a heterotachy mixture model accounting for heterotachous evolution — rate heterogeneity among sites and lineages. This version can be downloaded from here:
http://www.iqtree.org/#variant
A user guide is available at http://www.iqtree.org/doc/Complex-Models#heterotachy-models.
Please note that this is still a pre-release version — so suggestions and feedback are welcome!
Jul 15, 2016 Release
This version fixes various problems improving software stability.
New features:
-madd option (requested by David Kerk).CF4 of Wang et al. (2008) now includes Gamma rate heterogeneity by default.--sequential to read sequential phylip alignment file format.Bug fixes:
-wbtl option (reported by Teo).-mtree for partition finding (reported by a web user).Jun 29, 2016 Publication
D. Schrempf, B.Q. Minh, N. De Maio, A. von Haeseler, and C. Kosiol (2016) Reversible polymorphism-aware phylogenetic models and their application to tree inference. J. Theor. Biol., in press. http://dx.doi.org/10.1016/j.jtbi.2016.07.042
The associated IQ-TREE PoMo version and user guide are available at:
http://www.iqtree.org/#variant
Highlights
- Species tree inference from genome-wide population data.
- Takes incomplete lineage sorting into account.
- Analytical solution of stationary distribution and formal proof of reversibility.
- Reversibility ensures swiftness and stability.
- Increase of sample size per species improves estimations without raising runtime.
- Comparison to the Wright-Fisher diffusion.
Abstract: We present a reversible Polymorphism-Aware Phylogenetic Model (revPoMo) for species tree estimation from genome-wide data. revPoMo enables the reconstruction of large scale species trees for many within-species samples. It expands the alphabet of DNA substitution models to include polymorphic states, thereby, naturally accounting for incomplete lineage sorting. We implemented revPoMo in the maximum likelihood software IQ-TREE. A simulation study and an application to great apes data show that the runtimes of our approach and standard substitution models are comparable but that revPoMo has much better accuracy in estimating trees, divergence times and mutation rates. The advantage of revPoMo is that an increase of sample size per species improves estimations but does not increase runtime. Therefore, revPoMo is a valuable tool with several applications, from speciation dating to species tree reconstruction.
Apr 15, 2016 Release
New features:
-lmap ALL option (requested by Karen Meusemann).Bug fixes:
-m TESTMERGE when all partitions are merged into one (reported by Tan Mun Hua).-m TESTNEW for Windows version only (reported by Giorgio Matassi).Apr 15, 2016 Publication
O. Chernomor, A. von Haeseler, and B.Q. Minh (2016) Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices. Syst. Biol., 65, in press.
http://dx.doi.org/10.1093/sysbio/syw037
Abstract: In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary model. Although partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search algorithms due to the existence of phylogenetic (partial) terraces. Here, we introduce the phylogenetic terrace aware (PTA) data structure for the efficient analysis under partition models. In the presence of missing data PTA exploits (partial) terraces and induced partition trees to save computation time. We show that an implementation of PTA in IQ-TREE leads to a substantial speedup of up to 4.5 and 8 times compared with the standard IQ-TREE and RAxML implementations, respectively. PTA is generally applicable to all types of partition models and common topological rearrangements thus can be employed by all phylogenomic inference software.
Apr 2, 2016 Publication
J. Trifinopoulos, L.-T. Nguyen, A. von Haeseler, and B.Q. Minh (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res., 44, W232-W235. http://dx.doi.org/10.1093/nar/gkw256
The associated IQ-TREE web server is available at:
http://iqtree.cibiv.univie.ac.at
Abstract: This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology) in common alignment formats and a wide range of evolutionary models including mixture and partition models. W-IQ-TREE performs fast model selection, partition scheme finding, efficient tree reconstruction, ultrafast bootstrapping, branch tests, and tree topology tests. All computations are conducted on a dedicated computer cluster and the users receive the results via URL or email. W-IQ-TREE is available at http://iqtree.cibiv.univie.ac.at. It is free and open to all users and there is no login requirement.
Mar 16, 2016 Release
Fix bugs introduced in 1.4.0:
-mtree option (reported by a web server user).New features:
-lmclust) in RAxML-style format for likelihood mapping analysis.--opt-gamma-inv to optimize +I+G parameters thoroughly.Mar 7, 2016 Phd dissertation
Congrats to Lam-Tung Nguyen! He just successfully defended his PhD dissertation today entitled:
Computational methods for fast and accurate phylogenetic inference
Mar 4, 2016 Release
New features:
Bug fixes:
Special thanks to Karen Meusemann and Giap Nguyen for testing the beta versions. Download version 1.4.0 from GitHub
Feb 12, 2016 Opinion
A user opinion on IQ-TREE:
The results look promising with tree topology, branch length, and support values showing broad correlation (see below for data). The fact that this is an actively developed piece of software, with good documentation and some good peer reviewed papers gives me confidence to try this for the next few phylogenetic analyses I need to run.
Read the original article here:
http://bitsandbugs.org/2016/01/25/iqtree-vs-raxml-for-phylogenetic-tree-construction/
Jan 28, 2016 Release
Bug fixes:
Jan 19, 2016 Release
Bug fixes:
A crash when performing analysis on partitioning schemes produced by the k-means algorithm of PartitionFinder (reported by Pete Hosner). This is due to a partition containing only constant sites and the other partitions containing only variable sites. Such partitioning schemes are not recommended for phylogenetic analysis and users are advised to consult PartitionFinder author.
A crash with too high or too low rates for FreeRate model (reported by Hermes Escalona and Adrian Arellano Davin).
Dec 17, 2015 Phd dissertation
Congrats to Olga Chernomor! She just successfully defended her PhD dissertation today entitled:
Phylogenomics: theory, algorithms and applications
Also available at university library: http://othes.univie.ac.at/39935/
Dec 10, 2015 Release
New features:
-blmin and -blmax option for min and max branch length (requested by Hang Phan).-wslm and -wslmr options to print site log-likelihood per mixture class and per mixture+rate category, respectively (requested by Huaichun Wang).--link-alpha option to link Gamma shape parameter (alpha) across partitions (requested by Huaichun Wang).Bug fixes:
+ASC model for protein data: disabled now by default (reported by several web server users and Lars Jermiin).-z and -sp when changing to old kernel.-t RANDOM initial model parameters will now be estimated on a parsimony tree (thanks to Jesse Breinholt for the report and suggestion).Other changes:
~ as an unknown character in the alignment.Nov 19, 2015 Announcement
We are happy to announce the launch of the new IQ-TREE web site immediately available at the same URL:
http://www.cibiv.at/software/iqtree
Notably we updated extensive online user documentation for using IQ-TREE including quick start guide, tutorials, command reference, maximum likelihood models and compilation guide. This is to replace the outdated pdf manual.
The IQ-TREE source code is now hosted at github:
https://github.com/Cibiv/IQ-TREE
for developers’ convenience.
Oct 16, 2015 Release
We are pleased to announce version 1.3.10 with following changes:
+ASC] model causing incorrect branch length estimates (thanks to Marcus Teixeira for reporting it).Sep 29, 2015 Release
We are pleased to announce version 1.3.9 with following notable changes:
+R] and LG4X model. Special thanks to Edward Susko, Thomas Wong and Lars Jermiin.-wbtl to write bootstrap tree file (.ufboot) with branch lengths.-madd to include mixture models into model selection procedure (e.g. -madd LG4M,LG4X).-alrt 0 to perform the parametric approximate likelihood ratio (aLRT) branch test (Anisimova and Gascuel, 2006).-abayes to perform the parametric aBayes branch test (Anisimova et al., 2011).Aug 29, 2015 Publication
Congrats to Olga for an ultrafast acceptance of her paper (Chernomor et al., 2015) at Journal of Computational Biology. It was accepted just after 8 days of submission!
Abstract: In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original “full” terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.”
Further reading:
O. Chernomor, B.Q. Minh, and A. von Haeseler (2015) Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference. J. Comput. Biol., in press. (DOI: 10.1089/cmb.2015.0146, PMID: 26448206)
Aug 26, 2015 Release
-m TEST (model testing) and -spp/-spj (edge-linked partition model) within one run.Aug 23, 2015 Release
Version 1.3.7 is released with following changes:
-m TESTNEW).-suptag (used with -sup) when assigning support values from a set of input trees into a given tree, each tagged branch in the given tree will be assigned values of form support@tree1@tree2@...@treeK, corresponding to the IDs of the input tree where this branch occurs (requested by Max Maronna).-t RANDOM to start tree search from a random starting tree (requested by Karen Meusemann).Aug 15, 2015 Release
Version 1.3.6 is released with following substantial changes:
+I+G is added back into the candidate model list of new model selection procedure (-m TESTNEW).cmake -DIQTREE_FLAGS=static source_dirJul 24, 2015 Release
Version 1.3.5 is released with a few fixes (thanks to Lars Jermiin for finding two issues with model selection):
-mtree) now prints final tree corresponding to best-fit model.-m TESTNEW)..iqtree report file now includes log-likelihood of consensus tree and Robinson-Foulds distance between found ML tree and consensus tree.Jul 10, 2015 Release
Version 1.3.4 is released with the following fixes:
+ASC]-spp with -m TESTMERGE.+FO]. Fix memory deallocation when using -m TEST for Windows version.Jun 27, 2015 Release
We are pleased to announce version 1.3.3 with substantial improvements:
-rcluster option to speed up analysis for data sets with many partitions (e.g., >100 partitions).-st NT2AA option).-wsi option).Jun 11, 2015 Release
We are pleased to announce version 1.3.2 with substantial improvements:
May 27, 2015 Release
-spp option)May 20, 2015 Release
We are pleased to announce version 1.3.0 with following major updates:
-m TESTNEW or -m TESTNEWONLY. Among others, it uses the FreeRate model (Yang, 1995; Soubrier et al., 2012) as replacement for the problematic I+G model. FreeRate model is also implemented in PhyML and BEAST 2.U (Selenocysteine; treated as unknown character) and J (I or L).Apr 8, 2015 Release
+I model rate normalization.assert(new_tree_lh >= tree_lh - 10.0).-m TEST option with standard bootstrap.Mar 4, 2015 Release
-mset m1,...,mk to do model selection from a list of models.mtMAM model that unexpectedly stopped model selection.+I+G likelihood computation did not account for partially constant sites properly.Feb 17, 2015 Release
Feb 10, 2015 Release
We are pleased to announce the major update 1.2.0 with following new features:
C10,...,C60, EX2, EX3, EHO, UL2, UL3, EX_EHO, LG4M, LG4X, JTTCF4G)."MIX{HKY,TN}+G") or via a nexus file. Have a look at file models.nex in the bin folder of the release version.-fconst f1,...,fN to add a number of const patterns into alignment (N=#states)Dec 19, 2014 Release
Dec 7, 2014 Release
-m TESTLINK option+I modelNov 5, 2014 Release
-mset option to restrict model selection to models supported by RAxML (-mset raxml), MrBayes (-mset mrbayes), or Phyml/PartitionFinder (-mset phyml, -mset partitionfinder).Oct 23, 2014 Release
We are pleased to release the major update 1.1 with the following new enhancements:
Aug 29, 2014 Release
Patch version 1.0.1 fixes a bug where sometimes you saw on the screen ERROR / POSSIBLE BUG: logl=XXX < YYY Download version 1.0.1 from GitHub
Jul 28, 2014 Release
We are happy to announce the major release of IQ-TREE software version 1.0.0 with the following news:
-pll option and gives a speedup of 2X to 8X.-nni5) is now the default option because of its higher accuracy.Oct 20, 2013 Release
Beta version 0.9.6 and earlier versions:
-nni5 option (optimizing 5 branches around NNI). This comes at the trade-off of c.a. 2X longer running time.Olga's paper accepted at Systematic Biology
Parallel IQ-TREE MPI pre-release
IQ-TREE Heterotachy pre-release
PhD position in phylogenomic inference