Beta version 1.7-beta8

Bugfixes:

• Safe likelihood scaling for nonreversible models (requested by Vinh and Cuong).
• Eigen3 decomposition for MG-type codon model (reported by Nathanael Walker Hale).
• -nt AUTO with -S option.
• Crash with outgroup option (-o) for the new -S option (reported by Dan Vanderpool).
• Assertion about ordered_pattern when some partition has no variant sites (reported by Dan Vanderpool and Samuel Church).

IQ-TREE version 1.6.9

Bugfixes:

• IMPORTANT: Incorrect AU test p-values with partition models, introduced in v1.6.6 (reported by Ales Bucek).
• Crash in ModelFinder when having codon partitions with different genetic codes (reported by Morgan Jackson).
• Crash with multiple runs option (--runs) and -bnni (reported by Vanessa Vera Fain).

Other changes:

• Better error checking for nexus partition file to prevent mis-specifying comma and semi-colon (reported by Denis Jacob Machado).
• Safe writing checkpoint file via a temporary file (reported by Giuseppe Aprea and thanks Heiko).
• -rcluster-max activates relaxed clustering algorithm without having to specify -rcluster.
• --no-outfiles suppress .treefile as expected (reported by Cecile Ane).

Beta version 1.7-beta7

• Fix crash with --scf for rooted tree (reported by Aaron Liston).
• --cf-verbose to print details about gCF for each gene tree (.cf.stat_tree file) and sCF for each locus (.cf.stat_loci file).
• Parallelised sCF computation.
• --bisymtest-remove-bad[-good] will write .good.nex or .bad.nex partition file (requested by Renee Catullo).
• Ancestral sequence reconstruction (-asr) now works when there are absent state(s).
• Bug in eigen decomposition and matrix exponentiation for Lie Markov models.

Beta version 1.7-beta6

Support for concordance factor analysis. See
http://www.iqtree.org/doc/Concordance-Factor

Beta version 1.7-beta5

Notable new features:

• Much faster tree search under topological constraint.
• Partition option allows directory name to create a partition model of all alignment files in the directory.
• -S PARTITION | DIRECTORY to perform separate tree inference for each partition.
• --terrace to check if ML tree lies on a phylogenetic terrace (Biczok et al. 2018). Code from https://github.com/terraphast).
• --tbe to perform transfer bootstrap expectation (Lemoine et al. 2018). Code from https://github.com/evolbioinfo/booster.
• -m NONREV for general non-reversible models.
• --bisymtest to perform binomial test of symmetry (Naser et al. submitted).
• --mlrate to compute site rates by maximum likelihood (requested by Alex Dornburg and Jeff Townsend).
• --modelomatic to find best codon / protein / DNA models (Whelan et al. 2015).

New options:

• --root-find to find the root during model optimisation.
• --root-dist to optimise rooting position up to a certain distance (default: 2).
• --link-model to link substitution models across partitions.
• --model-joint MODEL to enforce joint model name for all partitions while rate heterogeneity is still unlinked.
• --init-model to specify initial rate matrix.
• --loop-model to specify number of loop iterations for partition model optimisation (default: 10).
• --no-seq-comp to disable sequence composition test.
• --estimate-model to estimate model params for tree evaluation with -z.

IQ-TREE version 1.6.8

Important change:

• AU test is now available again using maximum likelihood estimates of p-values. See #86 for full details.

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".

Patch version 1.6.7.2

Bugfixes:

• Crash with model selection for mixed data type (reported by Paul Frandsen).
• Crash with model selection when partitions <= 2 (reported by Michele Leocadio).
• Revive AU test (still experimental).

Beta version 1.7-beta4

• Allow partition models with non-reversible models.
• New option --modelomatic to find best codon, AA or DNA models (Whelan et al. 2015).
• Allow unlinked partition models (-spu) with bootstrap.
• New option --bisymtest-stat to print pairwise statistics of tests of symmetry (requested by Suha Naser).
• New option --permsymtest NUM to do permutation test of symmetry by Eric Stone (requested by Suha Naser).

Beta version 1.7-beta3

• New option --model-joint MODEL to enforce joint model name for all partitions while rate heterogeneity is still unlinked.
• Update Terraphast library (thanks Lukasz).
• Proper parsimony branch lengths by ancestral reconstruction.
• -bl-eval default to 1 (instead of 2) thanks to better parsimony branch lengths.
• Faster and SIMD kernel for Sankoff parsimony.
• Much faster parsimony with constraint tree.
• Parallel computation of parsimony trees.

Bugfixes:

• Crash with consensus construction for rooted trees.

Beta version 1.7-beta2

New options:

• Checkpointing while estimating linked model across partitions.
• --mlrate to compute site rates by ML (requested by Alex Dornburg and Jeff Townsend).
• --mpcost to input a cost matrix file for parsimony.
• -mset accepts string with prefix '+' to add a model into existing list.
• --estimate-model to estimate model params for tree evaluation with -z.
• --root-find to find the root during model optimisation.
• --support to print branch supports file.
• --bisymtest for binomial test of symmetry.
• Allow directory name for partition option to read all alignment files in the directory.
• --site-concordance to compute site concordance factor.

Bugfixes:

• Mixing rooted and unrooted trees with -spu option (reported by Cuong Dang).