Release Notes

IQ-TREE version 1.6.8

Oct 28, 2018

Important change:

Bugfixes:

  • Crash with model selection for mixed data type (reported by Paul Frandsen).
  • Crash with model selection when partitions <= 2 (reported by Michele Leocadio).
  • Reading non-reversible models from file.
  • Error message “A taxon has no name” to “Redundant double-bracket”.

Download latest version 1.6.8

IQ-TREE version 1.6.7.1

Sep 7, 2018

  • Show more precision in log likelihood with --show-lh (thanks Benjamin Redelings)
  • Reimplement -tina and -st MULTI option (requested by Ingo Ebersberger)

Bugfixes:

  • Crash at the end with --runs and partition model (reported by David Maddison)

Download version 1.6.7.1 from GitHub

IQ-TREE version 1.6.7

Aug 23, 2018

Important changes:

  • Temporarily disable AU test due to unresolved numerical issue when bp-rell are all zeros.

Bugfixes:

  • Checkpointing issue in ModelFinder for mixture models causing incorrect likelihoods with e.g. -madd C10 (reported by Juergen Strassert).
  • Checkpointing Lie Markov models.
  • (v1.6.6) Incomplete parsing of site positions of partition file (reported by Alexey Kozlov).
  • Parsing polymorphic states from NEXUS file (reported by Steven Heritage).
  • Use of only 1 thread when #partitions < #cores (reported by Alexey Kozlov).
  • Double RAM usage for -bnni option (reported by Juergen Strassert).
  • Over-bound for optimizeTreeLengthScaling causing too long branch lengths in extreme cases (reported by vikaszsi77).
  • Exclude ORDERED model by default for morphological data due to frequent numerical underflow.
  • (v1.6) -m ..MERGE.. wrong concatenateAlignments with missing data (reported by David Dunchene).
  • Error message instead of crash when using -bsam with non-partition model (reported by Sarah Jensen).

Download version 1.6.7 from GitHub

IQ-TREE version 1.6.6

Jul 1, 2018

This version contains a number of bugfixes and is highly recommended for all users.

Bugfixes:

  • Issue with internal tree node names changed from slash to underscore (reported by JP Flandrois).
  • Wrong FREQ_UNKNOWN assertion with protein mixture models, e.g. LG4X (reported by Giddy Landan).
  • Disallow specifying both --runs with -lmap option (reported by Giap Nguyen).
  • Reading nexus polymorphic characters for non-DNA data (reported by a web user).
  • Amino-acid O (22nd amino-acid) is accepted as missing data (reported by Cuong Dang).
  • Negative initial free-rates in rare cases (reported by Paul Frandsen).
  • Memory leak in reading NEXUS alignment.
  • Crash with resampling strategy (-bsam) for standard bootstrap (-b) and jackknife (-j option).
  • Crash with standard bootstrap and partition merging (-m ...MERGE) (reported by Guoqing Li).
  • Wrong error with codon models and -t RANDOM (reported by Karen Meusemann).
  • Parsing error with blank chars in partition file (reported by David Maddison).
  • Freezing caused by old Intel OpenMP library (reported by David Maddison).
  • Too strict assertion about one applied NNI (reported by Karen Meusemann).
  • Error message when specifying mixture with GHOST model (reported by Anja Spang).

Download version 1.6.6 from GitHub

IQ-TREE version 1.6.5

May 8, 2018

Bugfixes:

  • GTR20 protein model does not optimise rate parameters.
  • Replace odd characters in taxon names in tree file by underscore as done with alignment file (issue #31).
  • Replace odd characters in taxon names in cluster file by underscore (issue #54).
  • Crash with combination of bootstrap (-b option), partition model (-spp) and model testing (-m TEST) at the phase of analysing original alignment (reported by paul.madeira).

Download version 1.6.5 from GitHub

IQ-TREE version 1.6.4

Apr 30, 2018

News:

  • New option --runs to 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.
  • Print branch lengths scaled in number of substitutions for PoMo models.
  • Support specifying 6 GTR rates and G-T rate to be zero from command line (requested by Ben Redelings).
  • New option --show-lh to compute tree log-likelihood without parameter optimisation (issue #67).

Bugfixes:

  • Fix compilation with gcc 4.8.
  • Incorrect parsing +P for PoMo model string (thanks Carolin Kosiol).
  • Issue #66: Incorrect frequency mixture model when coupled with GTR20 (reported by Dominik Schrempf).
  • .ufboot trees file contains partial branch supports by combination of -bb and -alrt (reported by Guifre Torruella Cortes).
  • Crash in likelihood computation for +ASC model when some states are rare (reported by Paul Madeira).
  • Numerical instability for codon models by reducing upper bound of omega/kappa from 100 to 50 (reported by Aleksas Lab).
  • Crash reading DNA model from file (reported by Benjamin Redelings).
  • Crash with -z option with rooted trees in the presence of identical sequences (reported by cjp1043).

Download version 1.6.4 from GitHub

IQ-TREE version 1.6.3

Mar 22, 2018

This version improves software stability and highly recommended to update for all users.

Bugfixes:

  • Abort in ModelFinder when a user tree is supplied via -t option.
  • Erroneous message “leaves and taxa_set do not match” by rooted user tree (-t) and partition model (reported by Dieter Waechter).
  • Abort in ModelFinder by -sp option (edge-unlinked) and -mtree.
  • Error-checking partition with identical names.
  • Crash with rooted user trees via -z option.
  • Change ERROR about Too many iterations in tqli to WARNING.
  • Abort with combination of -nt AUTO and -mtree (reported by Mark Miller).
  • Crash with -bnni and -spp by temporarily turning on NNI5 instead of NNI1 (originally reported by Xiaofan).
  • Quitting by mixed data types (reported by Stephen Baca).
  • Crash with numerical underflow for lh-branch (reported by Karen Siu Ting).

New features:

  • -ntmax option to specify maximum number of threads by -nt AUTO option (requested by @sjspielman).
  • SH-aLRT test is now parallelised over multiple cores (requested by Heiner Kuhl).
  • Support GTR model for multistate data (requested by Sergio Andres Munoz Gomez).
  • Support jackknife with new option -j (requested by Emmanuel Toussaint).
  • New option -version to display version number (requested by David Maddison).

Download version 1.6.3 from GitHub

IQ-TREE version 1.6.2

Mar 1, 2018

Bugfixes:

  • Fix a thread-unsafe bug during partition merging of ModelFinder (reported by Karen Meusemann and Marianne)
  • Fix infinite hanging by LG+C10 or similar models (reported by Craig Herbold)
  • Fix parsing -net option (reported by Cameron Weadick)
  • Fix error message for -fast and -bb

New features:

  • Support reading non-reversible protein Q matrix from a file.
  • New option --write-branches to write branch lengths of tree (and partition trees) into .branches.csv file (requested by Rob Lanfear)
  • Allow -o option to specify a comma-separated list of outgroup taxa (requested by Andrew Roger)

Download version 1.6.2 from GitHub

IQ-TREE version 1.6.1

Dec 29, 2017

Bugfixes:

  • Memory unalignment in likelihood kernel when the number of states is odd (Thanks @vinuesa)

Download version 1.6.1 from GitHub

IQ-TREE version 1.6.0

Dec 23, 2017

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 iqtree.

Notable new features:

  • Polymorphism-aware models accounting for incomplete lineage sorting (code contributed by Dominik Schrempf).
  • Lie Markov and non-reversible models (code contributed by Michael Woodhams).
  • Heterotachy models accounting for rate variation across sites and lineages.
  • ModelFinder is redesigned to be more flexible. ModelFinder now supports edge-linked partition model selection. It also allows Lie Markov models, heterotachy (+H) models, PoMo models. ModelFinder now uses checkpoint file .model.gz to save space.
  • Xeon Phi Knights Landing (AVX-512) support with 2X or more speedup.
  • New option -fast to match the speed of FastTree program while still obtaining better trees.
  • New option -bnni to further optimize UFBoot trees by nearest neighbor interchange (NNI) directly on corresponding bootstrap alignments (UFBoot2+NNI).
  • New option -asr for ancestral sequence reconstruction written to .state file.
  • New option -rclusterf to perform fast relaxed clustering algorithm of PartitionFinder2.
  • New option -rcluster-max to limit maximum number of partition pairs for merging with rcluster algorithm.

New features:

  • New option -alninfo to print alignment sites statistics to .alninfo file (requested by Federico Gaiti).
  • For PMSF first fitting step: increase epsilon from 0.01 to 0.1, leading to 2x-3x speedup.
  • New option -czb to collapse zero branches, useful by bootstrapping with polytomy.
  • For standard bootstrap, branch lengths of consensus tree are now optimized on original alignment (requested by Tim).
  • Report mixture model component in .iqtree file if necessary (requested by Joran Martijn).
  • Three new mitochondrial protein matrices mtMet, mtVer, mtInv (https://doi.org/10.1186/s12862-017-0987-y). Code contributed by @cuongbb.
  • Support alignments in gzipped format.
  • -wql option now prints quartet area and corner in .quartetlh file (requested by Karen Meusemann).
  • Support GENE resampling (-bspec GENE) and GENESITE resampling (-bspec GENESITE) for standard bootstrap with partition models.

New features for PoMo models:

  • Allow PoMo plus Gamma rate model (+P+G).
  • Allow bootstrapping with PoMo.
  • Improved numerical stability.

Download version 1.6.0 from GitHub

IQ-TREE version 1.5.6

Dec 4, 2017

This version improves software stability and contains bugfixes:

  • Improved numerical stability when some state is absent from the alignment, especially with codon or morphological data.
  • Allow reading morphological and codon model from file in PAML format.
  • -mset option works with binary and morphological models.

Bugfixes:

  • Bug for multifurcating tree with multithreading (reported by Filipe Romero).
  • Crash when number of partitions > 2^15 (reported by Adela RoaVaron).
  • In Windows: Exit gracefully instead of abort when input file does not exist.
  • Exit gracefully instead of segfault when log file cannot be written.
  • Crash when constraint tree contains identical sequence which was removed (reported by Russell Minton).
  • Exit gracefully instead of abort about too many threads for too short alignment.
  • Exit gracefully instead of abort when outgroup taxon (-o option) does not appear in alignment.

Download version 1.5.6 from GitHub

IQ-TREE version 1.6.beta3

Jun 2, 2017

We are pleased to release the beta version 1.6.beta (available at http://www.iqtree.org) with many new cool features. During this beta-testing phase, feedback is much appreciated.

Notable new features:

  • Polymorphism-aware models accounting for incomplete lineage sorting (code contributed by Dominik Schrempf).
  • Lie Markov and non-reversible models (code contributed by Michael Woodhams).
  • Heterotachy models accounting for rate variation across sites and lineages.
  • Xeon Phi Knights Landing (AVX-512) support with 2X or more speedup.
  • New option -fast to match the speed of FastTree program while still obtaining better trees [Experimental].

New features:

  • -wql option now prints quartet area and corner in .quartetlh file (requested by Karen Meusemann).
  • Support GENE resampling (-bspec GENE) and GENESITE resampling (-bspec GENESITE) for standard bootstrap with partition models.
  • Sequential and multicore versions are merged, thus iqtree-omp executable becomes iqtree.

Download version 1.6.beta3 from GitHub

IQ-TREE version 1.5.5

Jun 2, 2017

New features:

  • Support gene-resampling (-bsam GENE) and gene-site-resampling (-bsam GENESITE) for standard bootstrap with partition models.
  • Support and treat polymorphic characters in (...) or {...} notation as missing data (requested by Steven Heritage).
  • Improved numerical stability for codon models (reported by Giorgio Matassi, Sarah Mathews, Ricardo Alves). Note that numerics may still fail if many codons are absent in the data.
  • Do not test ascertainment bias correction (+ASC) for codon models by default (thanks Ricardo Alves).
  • Only reduce minimal branch length for long alignment and un-partition models (thanks to Steven Mussmann).

Bugfixes:

  • Initial tree generation problem with constrained tree search option -g.
  • Likelihood underflow for large multifurcating trees (e.g. consensus tree) (reported by Giap Nguyen).
  • Crash with -minsupnew option (reported by Longzhi Tan).
  • Compilation with gcc under Mac (thanks @ilovezfs).
  • Crash with -nni1 for partition model -spp (reported by Diep Thi Hoang).

Download version 1.5.5 from GitHub

IQ-TREE version 1.5.4

Apr 3, 2017

Important changes:

  • If no model is specified via -m, IQ-TREE will perform the new model selection, ModelFinder (MF). Accordingly, two new options are introduced: -m MF (equivalent to -m TESTNEWONLY) and -m MFP (equiv. to -m TESTNEW). For backward compatibility TESTNEW will still be available but might be removed in a future release.
  • Combining standard bootstrap (-b) and constraint tree option (-g) will impose the constraint on bootstrap trees (previously not). Thanks to Matthew Prebus for discussions.

New features:

  • The precompiled Linux executables are now backward compatible with the old Linux kernel 2.X, which resolves the error message “FATAL: kernel too old”.
  • Support input files with different newline formats to resolve conflicts between Mac, Windows or Linux files.
  • For data sets with identical sequences, redundant sequences are ignored. However, IQ-TREE will now keep two identical sequences (i.e. if five sequences A,B,C,D,E are identical to each other, then A,B are kept and C,D,E are ignored). This avoids incompatibility between bootstrap and non-bootstrap runs.
  • Warning about too many threads for short alignments (reported by Joran Martijn).
  • New option -wbsf to print individual bootstrap alignments and sitefreq files for standard bootstrap (requested by Huaichun Wang).

Bug fixes:

  • Segfault caused by combining standard bootstrap, partition model and constraint tree (reported by Matthew Prebus).
  • Crash by -nni1 option (reported by Carlos Rivera).
  • Illegal instruction on older Mac which does not support AVX instruction set (reported by Richard Moir and Matthew Fullmer).
  • Crash when combining -mtree and -bb during model selection (reported by Chris Buddenhagen).

Download version 1.5.4 from GitHub

IQ-TREE version 1.5.3

Jan 16, 2017

Version 1.5.3 improves software stability. We thank a lot to all users mentioned below for the reports.

Bug fixes:

  • Crash for +R+ASC model (reported by olaf.thalmann).
  • Improper multiple restart for I+G model optimization (reported by 98w8h1).
  • For large data sets with many sequences:
    • Incorrect handling of numerical underflow when all state likelihoods are zero (reported by Gerhard Jaeger).
    • Numerical underflow for invariant sites (reported by ledum_laconicum, kelly.schiro).

Other changes:

  • Invariable (+I) site model now considers ambiguous constant sites.
  • -wba (write bootstrap alignments) works now with standard bootstrap (-b).

Download version 1.5.3 from GitHub

IQ-TREE version 1.5.2

Dec 3, 2016

This version improves software stability. We thank a lot to all users mentioned below for the reports.

Bug fixes:

  • Incorrect likelihood computation under safe mode for rate homogeneity models (thanks to Ricardo Alves).
  • Bug when finally merging partitions (-m TESTMERGE) (reported by Olivier Navaud).
  • Crash when computing distance with consensus tree in presence of identical sequences (-bb option) (reported by Julien).
  • Crash for I+G model when p-invar close to 0 (reported by liqiangj, Frank Wright).
  • Bug likelihood scaling for ASC model (reported by lgrismer).

Other changes:

  • Fix misleading message about multifurcating trees (reported by Noah Simons).
  • Incompatibility problem with older Mac by switching back to libstdc++ instead of libc++ (reported by Matthew Fullmer).
  • Fix compilation issue for BSD and newer GCC 5.4 (thanks to @njoly).
  • Improved -nt AUTO option, e.g. to work with model selection (reported by Remi Denise).

Download version 1.5.2 from GitHub

IQ-TREE version 1.5.1

Nov 8, 2016

We are pleased to announce version 1.5.1 with special focus on huge data sets and supercomputing with following new features:

  • Merged the parallel MPI version with much better parallel efficiency and scalability. The old MPI version is deprecated.
  • Memory saving mode via a new -mem option to restrict RAM usage, helpful for complex mixture models. For example, -mem 64G to use at most 64 GB. By default, IQ-TREE will try to fit the computer RAM size. Note that this mode does not work with partition models yet.
  • Safe numerical mode for huge data sets to avoid “Numerical underflow” errors. This mode is automatically turned on when having more than 2000 sequences. It can be manually turned on via -safe option.
  • New option -nt AUTO to automatically determine best number of threads in multicore version.
  • Support AVX2 instructions.

Download version 1.5.1 from GitHub

IQ-TREE version 1.5.0a

Oct 31, 2016

This is a hot fix for -g option in version 1.5.0:

  • A bug when computing initial constrained trees (-g option) and recovering from checkpoint (thanks to Xingxing Shen for the report).

Download version 1.5.0a from GitHub

IQ-TREE version 1.5.0

Oct 24, 2016

We are pleased to announce IQ-TREE version 1.5.0 with following major updates:

Major new features:

  • A new posterior mean site frequency (PMSF) model as a rapid approximation to the time and memory consuming CAT profile mixture models C10 to C60 (Le et al., 2008a). The PMSF model is much faster and requires much less RAM than the mixture models, regardless of the number of mixture classes. This allows, for the first time, to conduct nonparametric bootstrap under such complex models. Our extensive simulations and empirical deep-phylogeny data analyses demonstrate that the PMSF models can effectively ameliorate long branch attraction artefacts. For details see http://www.iqtree.org/doc/Complex-Models#site-specific-frequency-models

  • New option -g to supply a user-defined constraint tree, which will guide subsequent tree search. The constraint tree can be multifurcating and need not to include all taxa.

Bug fixes:

  • Crash with zero weights of mixture models for short alignments (thanks to Laura Eme for the report).
  • Incorrect site rate file (-wsr option) in the presence of identical sequences (thanks to Brian Foley for the report).
  • Memory overflow for tree topology testing for extremely long alignments (>500,000 sites) (thanks to Karen Meusemann for the report).
  • Rare issue with multifurcating trees and partition model (thanks to Xingxing for the report).

Other changes:

  • A new biologist-familiar example data file example.phy, which contains mitochondrial DNAs of human, gorilla, dog, mouse, etc. The data set was taken from the phylogenetic handbook (thanks to Brian Foley for suggestion).
  • Printing an alignment with suffix .varsite with only variable sites if ascertainment bias correction (ASC) is not applicable.
  • New option -wpl to write partition-specific log-likelihoods to .partlh file (requested by Karen Meusemann).

Download version 1.5.0 from GitHub

IQ-TREE version 1.4.4

Aug 28, 2016

New features:

  • Allowing mixture frequency model with optimized frequency via e.g. -m C10+FO (requested by Edward Braun).
  • Supporting GTR20 (general time reversible) amino-acid model (requested by Desmond Ramirez, Panagiotis Adam).
  • New option -blscale to optimize tree length scaling factor and model parameters for a user tree passed via -t option (requested by Rob Lanfear). The results are written to .blscale file in YAML format.
  • New option --no-outfiles to suppress printing all output files (.log, .treefile, .iqtree files).

Bug fixes:

  • (critical) Memory overflow for long alignments (>55,000 aa site patterns) under large mixture models (e.g. C60) (reported by Matthew Brown).
  • (critical) AU test implementation (reported by Jan Janouskovec).
  • Counting of constant sites with many ambiguous states (reported by Greg Owens).

Download version 1.4.4 from GitHub

IQ-TREE version 1.4.3

Jul 15, 2016

This version fixes various problems improving software stability.

New features:

  • Better parameter estimates for I+G model.
  • More flexible mixture models for model testing with -madd option (requested by David Kerk).
  • The protein mixture model CF4 of Wang et al. (2008) now includes Gamma rate heterogeneity by default.
  • Support invariable sites plus FreeRate [+I+R] model (requested by Lars Jermiin).
  • New option --sequential to read sequential phylip alignment file format.

Bug fixes:

  • Failture too estimate too extreme GTR rate parameters (reported by Stephen Crotty).
  • Bug with likelihood scaling for constant sites under invariable site [+I] model (reported Remi Denise).
  • Crash with optimizing codon model parameters (reported by Xiaofan Zhou).
  • Redundant codon models for model selection (reported by Xiaofan Zhou).
  • Segfault caused by unaligned memory for partition model with binary data (reported by Marek L. Borowiec).
  • Crash with -wbtl option (reported by Teo).
  • Crash with -mtree for partition finding (reported by a web user).
  • A rare bug in NNI hill-climbing search.
  • A bug in printing .rate file via -wsr option (reported by Tim McInerney).
  • Several other minor issues.

Download version 1.4.3 from GitHub

IQ-TREE version 1.4.2

Apr 15, 2016

New features:

  • Ability to draw all unique quartets for likelihood mapping with -lmap ALL option (requested by Karen Meusemann).

Bug fixes:

  • A rare bug in -m TESTMERGE when all partitions are merged into one (reported by Tan Mun Hua).
  • A segfault in -m TESTNEW for Windows version only (reported by Giorgio Matassi).
  • A rare crash with partition model parameter estimation.
  • A bug in parsing semi-empirical codon model name (reported by Xiaofan Zhou).
  • A rare crash when sequence names are IDs.

Download version 1.4.2 from GitHub

IQ-TREE version 1.4.1

Mar 16, 2016

Fix bugs introduced in 1.4.0:

  • A crash with checkpointing for -mtree option (reported by a web server user).
  • A crash with likelihood mapping for partition models with sparse supermatrix (reported by Harald Letsch).

New features:

  • Support cluster file (-lmclust) in RAxML-style format for likelihood mapping analysis.
  • Support alignments with >255 sequences for likelihood mapping analysis.
  • New option --opt-gamma-inv to optimize +I+G parameters thoroughly.

Download version 1.4.1 from GitHub

IQ-TREE version 1.4.0

Mar 4, 2016

New features:

Bug fixes:

  • Fix a rare numerical issue when computing maximum likelihood distances for codon models (reported by Giap Nguyen)

Special thanks to Karen Meusemann and Giap Nguyen for testing the beta versions.

Download version 1.4.0 from GitHub

IQ-TREE version 1.3.13

Jan 28, 2016

Bug fixes:

  • Fix a numerical underflow with ascertainment bias correction [+ASC] model for large data sets (reported by Alex Riedel)

Download version 1.3.13 from GitHub

IQ-TREE version 1.3.12

Jan 19, 2016

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).

Download version 1.3.12 from GitHub

IQ-TREE version 1.3.11

Dec 10, 2015

New features:

  • For long alignments (>100,000 sites) the minimal branch length is now reduced to 0.1/alignment_length to accommodate analysis of very closely related sequences (thanks to David Wyllie for testing).
  • New -blmin and -blmax option for min and max branch length (requested by Hang Phan).
  • New -wslm and -wslmr options to print site log-likelihood per mixture class and per mixture+rate category, respectively (requested by Huaichun Wang).
  • New --link-alpha option to link Gamma shape parameter (alpha) across partitions (requested by Huaichun Wang).

Bug fixes:

  • Numerical problems with +ASC model for protein data: disabled now by default (reported by several web server users and Lars Jermiin).
  • Fix a rare crash for option combination -z and -sp when changing to old kernel.
  • Fix a crash with multicore version with own parsimony kernel (reported by Joan).
  • Fix a minor issue when outputting mixture model name in model testing (reported by Sophie Abby).
  • Fix a numerical problem with model testing (reported by Jana).
  • For -t RANDOM initial model parameters will now be estimated on a parsimony tree (thanks to Jesse Breinholt for the report and suggestion).

Other changes:

  • Windows AVX version (reported by Aaron Dickey) crashed due to a stack unalignment issue of TDM-GCC compiler (thanks to Agner Fog for suggestion). As a solution, all Windows binaries are now built with Clang.
  • Updated the latest vectorclass library of Agner Fog.
  • Print error instead of abort when applying branch tests for multifurcating trees.
  • Implement EM algorithm for mixture+FreeRate model.
  • Accept ~ as an unknown character in the alignment.
  • Code optimization resulting in 5%-10% reduction in running time.

Download version 1.3.11 from GitHub

IQ-TREE version 1.3.10

Oct 16, 2015

We are pleased to announce version 1.3.10 with following changes:

  • Support unlimited number of partitions for partition model analysis (no complaint about PLL_NUM_BRANCHES anymore).
  • Improved support for mixture models.
  • Fix a bug in ascertainment bias correction [+ASC] model causing incorrect branch length estimates (thanks to Marcus Teixeira for reporting it).
  • Fix a rare bug when branch lengths are close to upper bound (thanks to Huaichun Wang for reporting it).

Download version 1.3.10 from GitHub

IQ-TREE version 1.3.9

Sep 29, 2015

We are pleased to announce version 1.3.9 with following notable changes:

  • Several bug fixes improving software stability. Special thanks to Xiaofan, Karen Meusemann, Jozsef Bakonyi, Renee, Peter Hosner for reporting bugs.
  • A more stable expectation-maximization (EM) algorithm is implemented to optimize parameters of the FreeRate [+R] and LG4X model. Special thanks to Edward Susko, Thomas Wong and Lars Jermiin.
  • Several new features (requested by users):
    • Option -wbtl to write bootstrap tree file (.ufboot) with branch lengths.
    • Option -madd to include mixture models into model selection procedure (e.g. -madd LG4M,LG4X).
    • Option -alrt 0 to perform the parametric approximate likelihood ratio (aLRT) branch test (Anisimova and Gascuel, 2006).
    • Option -abayes to perform the parametric aBayes branch test (Anisimova et al., 2011).
  • Maximum number of partitions is increased to 16384 instead of 1024.

Download version 1.3.9 from GitHub

IQ-TREE version 1.3.8

Aug 26, 2015

  • Fix a bug introduced in 1.3.7 when using two options -m TEST (model testing) and -spp/-spj (edge-linked partition model) within one run.

Download version 1.3.8 from GitHub

IQ-TREE version 1.3.7

Aug 23, 2015

Version 1.3.7 is released with following changes:

  • Fix a bug introduced in 1.3.6 for new model selection procedure (-m TESTNEW).
  • Include L-BFGS-B algorithm (code taken from HAL_HAS package (Jayaswal et al., 2014) as the default to estimate model parameters. L-BFGS-B performs better than the previous BFGS implementation, for example, when optimizing LG4X and FreeRate models.
  • New option -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).
  • New option -t RANDOM to start tree search from a random starting tree (requested by Karen Meusemann).

Download version 1.3.7 from GitHub

IQ-TREE version 1.3.6

Aug 15, 2015

Version 1.3.6 is released with following substantial changes:

  • An expectation-maximization (EM) algorithm is implemented to optimize weights of mixture models (thanks to Huaichun Wang, Andrew Roger, Edward Susko for reporting initial issue on local optimum and providing this solution). The EM algorithm guarantees convergence on global optimum (Wang et al., 2008).
  • Fix an issue in reading morphological alignments (thanks to Max Maronna for reporting this).
  • +I+G is added back into the candidate model list of new model selection procedure (-m TESTNEW).
  • The starting phase of tree search now includes a BIONJ into the candidate tree set, which is sometimes better than parsimony trees.
  • Building from source code now generates dynamically linked binary. To build static binary, run cmake with e.g. cmake -DIQTREE_FLAGS=static source_dir

Download version 1.3.6 from GitHub

IQ-TREE version 1.3.5

Jul 24, 2015

Version 1.3.5 is released with a few fixes (thanks to Lars Jermiin for finding two issues with model selection):

  • Thorough model selection (-mtree) now prints final tree corresponding to best-fit model.
  • Fix slightly decreasing log-likelihood for more complex models during new model selection (-m TESTNEW).
  • For bootstrap: .iqtree report file now includes log-likelihood of consensus tree and Robinson-Foulds distance between found ML tree and consensus tree.

Download version 1.3.5 from GitHub

IQ-TREE version 1.3.4

Jul 10, 2015

Version 1.3.4 is released with the following fixes:

  • Fix support for ascertainment bias correction [+ASC]
  • For codon models, the site ranges are now counted on number of nucleotides instead of number of codons. When DNA and codon data are mixed in partition model, branch lengths are now interpreted as #nucleotide substitutions per nucleotide site. Note that for codon data, branch lengths are #nucleotide substitutions per codon site like PAML.
  • Fix usage of -spp with -m TESTMERGE.
  • Fix ML optimization of amino-acid frequencies [+FO]. Fix memory deallocation when using -m TEST for Windows version.

Download version 1.3.4 from GitHub

IQ-TREE version 1.3.3

Jun 27, 2015

We are pleased to announce version 1.3.3 with substantial improvements:

  • Implement the relaxed clustering algorithm of PartitionFinder with -rcluster option to speed up analysis for data sets with many partitions (e.g., >100 partitions).
  • Partition finding supports multicore now with linear speedup.
  • Increased multicore performance of partition model analysis.
  • Support direct translation of coding sequences into amino-acid (-st NT2AA option).
  • Adjust per-partition state frequencies for partition model such that the log-likelihoods are fully comparable with RAxML.
  • Print sequence identity scores along the tree (-wsi option).
  • Fix slow convergence of partition model parameter estimation with many partitions.
  • Fix memory allocation for large mixture models.

Download version 1.3.3 from GitHub

IQ-TREE version 1.3.2

Jun 11, 2015

We are pleased to announce version 1.3.2 with substantial improvements:

  • Memory requirement reduced by a factor of 3 (for example, from 60 GB down to 20 GB)
  • Increased performance of multicore version.
  • Increased performance of edge-linked partition models.
  • 32-bit version is available.

Download version 1.3.2 from GitHub

IQ-TREE version 1.3.1

May 27, 2015

  • Fixes a bug in rate optimization for edge-linked partition model (-spp option)

Download version 1.3.1 from GitHub

IQ-TREE version 1.3.0

May 20, 2015

We are pleased to announce version 1.3.0 with following major updates:

  • Support for ClustalW and MSF alignment file formats and RAxML-styled partition file format.
  • With Lars Jermiin group we developed a new model selection strategy, which is invoked via option -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.
  • Improved codon model implementation, which is more compatible with codonPhyML, e.g. including models of (Kosiol et al., 2007).
  • Codon model selection now allows up to 60 codon models to be tested!
  • Improved support for mixture models.
  • Accepting two new amino-acids: U (Selenocysteine; treated as unknown character) and J (I or L).
  • Several bug fixes, including a bug in FreeRate model optimization found and fixed by Thomas Wong and Lars Jermiin.

Download version 1.3.0 from GitHub

IQ-TREE version 1.2.3

Apr 8, 2015

  • Several bug fixes in codon model implementation.
  • Minor bug fix in +I model rate normalization.
  • Fix assertion assert(new_tree_lh >= tree_lh - 10.0).
  • Fix likelihood computation for binary, codon, morphological data.
  • Fix starting tree construction for binary, codon, morphological data.
  • Fix -m TEST option with standard bootstrap.

Download version 1.2.3 from GitHub

IQ-TREE version 1.2.2

Mar 4, 2015

  • New option -mset m1,...,mk to do model selection from a list of models.
  • Support for old Mac OS 10.5 (Leopard).
  • Bug fix: numerical issue with mtMAM model that unexpectedly stopped model selection.
  • Bug fix: +I+G likelihood computation did not account for partially constant sites properly.
  • Bug fix: optimization of branch lengths sometimes reduced tree likelihood (introduced in ver. 1.2.0).

Download version 1.2.2 from GitHub

IQ-TREE version 1.2.1

Feb 17, 2015

  • Fixes a bug introduced in ver. 1.2.0 causing incorrect SH-aLRT support values for large data sets.

Download version 1.2.1 from GitHub

IQ-TREE version 1.2.0

Feb 10, 2015

We are pleased to announce the major update 1.2.0 with following new features:

  • Supporting mixture models (C10,...,C60, EX2, EX3, EHO, UL2, UL3, EX_EHO, LG4M, LG4X, JTTCF4G).
  • User-defined mixture models via syntax (for example, "MIX{HKY,TN}+G") or via a nexus file. Have a look at file models.nex in the bin folder of the release version.
  • Joint and proportional partition models are now fully functional.
  • Automatical switching between SSE and AVX kernels depending on the current hardware. Thus, no separate executables are needed.
  • New option -fconst f1,...,fN to add a number of const patterns into alignment (N=#states)
  • Serveral bug fixes.

Download version 1.2.0 from GitHub

IQ-TREE version 1.1.5

Dec 19, 2014

  • Bug fix: Sometimes IQ-TREE enters an endless loop and will not stop.
  • Bug fix: when computing consensus tree from a partition analysis.

Download version 1.1.5 from GitHub

IQ-TREE version 1.1.4

Dec 7, 2014

  • Increasing max number of partitions to 512
  • Bug fix in -m TESTLINK option
  • Bug fix for +I model
  • Bug fix: Wrongly rounded protein model frequency in PLL
  • Bug fix for binary data

Download version 1.1.4 from GitHub

IQ-TREE version 1.1.3

Nov 5, 2014

  • Support FreeRate model for site rate heterogeneity (Experimental).
  • Added -mset option to restrict model selection to models supported by RAxML (-mset raxml), MrBayes (-mset mrbayes), or Phyml/PartitionFinder (-mset phyml, -mset partitionfinder).
  • Fix bug concerning removal of identical sequences.
  • Fix bug concerning +I model (+G and +I+G were not affected).

Download version 1.1.3 from GitHub

IQ-TREE version 1.1.0

Oct 23, 2014

We are pleased to release the major update 1.1 with the following new enhancements:

  • Under-the-hood code optimization for the default likelihood kernel, which gives a speedup up to 5X for DNA and 10X for protein alignments.
  • Support for Windows platforms and support GCC, Clang, MS Visual C++ and Intel C++ compilers.
  • Automatical handling of identical sequences in the alignment (no warnings about identical sequences anymore).
  • Bootstrap and tree search stopping rule combined for more accurate results.
  • Several bugs fixed.

Download version 1.1.0 from GitHub

IQ-TREE version 1.0.1

Aug 29, 2014

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

IQ-TREE version 1.0.0

Jul 28, 2014

We are happy to announce the major release of IQ-TREE software version 1.0.0 with the following news:

  • Integration of the phylogenetic likelihood library for fast likelihood computation. This is enabled via -pll option and gives a speedup of 2X to 8X.
  • A novel fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. It outperforms RAxML and PhyML in terms of log-likelihoods while requiring similar amount of computing time. A manuscript describing the new method was submitted.
  • NEW MODELS: codon models and ascertainment bias correction model for morphological or single-nucleotide-polymorphism (SNP) data.
  • Nearest neighbor interchange with five branch optimization (-nni5) is now the default option because of its higher accuracy.
  • SH-aLRT branch test also works now for partition models.

Download version 1.0.0 from GitHub

IQ-TREE version 0.9.6

Oct 20, 2013

Beta version 0.9.6 and earlier versions:

  • Ultrafast (partition) model selection for phylogenomic alignments.
  • Higher accuracy in tree reconstruction and bootstrap with more thorough nearest neighbor interchange enabled via -nni5 option (optimizing 5 branches around NNI). This comes at the trade-off of c.a. 2X longer running time.
  • Introduction of joint and proportional partition models to reduce the number of parameters in case of model overfitting (EXPERIMENTAL)
  • Introduction of gene-resampling and gene-and-site resampling for the bootstrap on multi-gene alignments.
  • Introduction of epsilon for ultrafast bootstrap: trees similar RELL log-likelihoods will be chosen at random to break tie. This helps to reduce over-optimistic supports in case of polytomies.
  • Tree topology tests (BP,KH,SH,ELW,WKH, and WSH tests via RELL method).
  • Partition models.
  • Parallel OpenMP version for multi-core CPUs.
  • New implementation of model selection that works for DNA, amino-acid, and binary models.

Download version 0.9.6 from GitHub

IQ-TREE releases