Beta version 1.6.beta5

NOTE: This version changes the checkpoint which is not compatible with any previous version! So use it with caution.

Bugfixes:

• Bug with bootstrap epsilon (-beps) which did not randomly choose almost equally ML trees. Thanks to @diepthihoang.
• Crash in the refinement step (-bnni) coupled with writing bootstrap trees (-wbt). Fixed by @diepthihoang.
• Fix in Lie Markov model checkpointing by @MichaelWoodhams.
• Incorrect error message about PoMo model with e.g. +POISSON model string. Fixed by @dschrempf.

New features:

• ModelFinder allows to test Lie Markov models.
• Three new mitochondrial protein matrices mtMet, mtVer, mtInv (https://doi.org/10.1186/s12862-017-0987-y). Code contributed by @cuongbb.

Beta version 1.6.beta4

Bugfixes:

• Incorrect SSE kernel assignment (thanks Diep).
• Failure compiling MPI version (thanks Ondrej Hlinka).

Beta version 1.6.beta3

New features:

• 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 -rcluster-max to limit maximum number of partition pairs for merging with rcluster algorithm.
• Support alignments in gzipped format.
• Merge changes from version 1.5.5.

Bugfixes:

• Crash with >32000 input partitions (reported by Adela RoaVaron).
• Issue with KNL (AVX-512) version.

IQ-TREE version 1.5.5

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).

Beta version 1.6.beta2

• Fix a crash in v1.6.beta with -m ...MERGE in the later stage of parsimony calculation (reported by Teo)
• Improve help messages for PoMo models.

Beta version 1.6.beta

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.

Bugfixes (inherited from 1.5.5-beta):

• 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).

IQ-TREE version 1.5.4

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).

IQ-TREE version 1.5.3

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).

IQ-TREE version 1.5.2

This version improves software stability. We thank 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).
• Uninitialized parsimony kernel (reported by ev.simonov).

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).

IQ-TREE version 1.5.1

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

• The parallel MPI version with better parallel efficiency and scalability, which allows to distribute IQ-TREE computations across different nodes/computers. See this guide to build iqtree-mpi.
• 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.