Beta version 1.6.3.b

News:

• Print branch lengths scaled in number of substitutions for PoMo.

Bugfixes:

• Various issues of --runs with other options.
• 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 due to too high upper bound of omega/kappa by reducing the bound from 100 to 50 (reported by Aleksas Lab).
• Modified error messages with too many threads (thanks David Maddison).

Beta version 1.6.3.a

NOTE: This is a beta version. Do not use unless you are asked to test it.

Bugfixes:

• Fix compilation with gcc 4.8.
• Incorrect parsing +P for PoMo model string (thanks Carolin).

New features:

• New option --runs to perform independent runs (requested by David Maddison).

IQ-TREE version 1.6.3

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).

IQ-TREE version 1.6.2

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)

Beta version 1.6.1.b

NOTE: This is a beta version. Do not use unless you are asked to test it.

Bugfixes:

• Fix a thread-unsafe bug during partition merging of ModelFinder (reported by Karen Meusemann and Marianne)
• Fix parsing -net option (reported by Cameron Weadick)
• Fix error message for -fast and -bb
• Towards fixing -bnni option with partition model (ongoing!)

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)

IQ-TREE version 1.6.1

This version fixes a bug with memory alignment in likelihood kernel when the number of states is odd.

Thanks @vinuesa for finding an early issue with previous commit.

IQ-TREE version 1.6.0

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.

Release candidate 1.6.rc2

This second release candidate for the 1.6 series fixes several issues in ModelFinder:

Bugfixes:

• Testing heterotachy models [+H].
• Crash with -mtree option.
• Crash with auto detect thread number [-nt AUTO].
• Crash with partition merging [MERGE in -m option].

Improvements:

• Support edge-linked partition finding (-spp or -q).
• New -rclusterf option that resembles rclusterf algorithm of PartitionFinder (simultaneous merging top 50% partition pairs).

Release candidate 1.6.rc

IMPORTANT CHANGE: 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.

New features (compared with 1.6.beta4):

• ModelFinder is redesigned to be more flexible. For example, it allows Lie Markov models, GHOST (+H) models, PoMo models. ModelFinder now uses checkpoint file .model.gz to save space.
• 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.

New features for PoMo models:

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

Bugfixes (compared with 1.6.beta4):

• Merge bugfixes from version 1.5.6.
• Checkpointing bug introduced in 1.6.beta5.
• Checkpointing with -bnni option (reported by Christopher Laumer).
• Wrong reporting of TreeLen by combination of -sp and -bb (reported by Sergio Andrés Muñoz Gómez).
• Crash when testing multi-thread efficiency for PMSF models (reported by Laura Eme).
• More robust optimization combing BFGS and L-BFGS-B (reported by Michael Woodhams).
• Bug with bootstrap epsilon (-beps) which did not randomly choose almost equally ML trees. Thanks to @diepthihoang.
• Fix in Lie Markov model checkpointing by @MichaelWoodhams.
• Incorrect error message about PoMo model with e.g. +POISSON model string. Fixed by @dschrempf.

IQ-TREE version 1.5.6

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.