October 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).

September 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.

August 26, 2015: Bug-fix version 1.3.8 is released:
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.

August 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 of Jayaswal et al. 2014; Syst Biol 63:726-742) 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).

August 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 and was described in Wang et al. (2008), BMC Evol. Biol. 8:331.
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"

July 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.

July 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.

June 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.

June 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.

Release version 1.3.0

Release version 1.1.2

Release version 1.1.3

Release version 1.1.4

Release version 1.1.5

Release version 1.2.0