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New features for PartitionFinder:

• Speed up PartitionFinder by "transferring" model parameter estimates to the merged partition pair.
• --merge-fast to only consider one model (GTR for DNA, LG for protein) for partition merging.
• --merge-fastest to further only consider +I+G rate model for partition merging.
• --merge-kmeans to perform k-means clustering of partition rates.
• --merge-log-rate to use log(rate) for clustering algorithm (incl. the relaxed clustering).

Robinson-Foulds distance:

• -rf1 treefile1 treefile2 to compute RF distances between corresponding k-th trees in two files.
• --normalize-dist to compute normalized RF distances.
• --out-csv to print .rfdist file in CSV format.

Bugfixes:

• Incorrect pairwise distance (.mldist file) with +I or +R rate models (reported by Sishuo Wang).
• Crash with -o option when the outgroup is identical to another sequence (reported by Yang Song).
• Crash in ModelFinder for mixed data types with edge-linked partition models -spp option (reported by Bernardo Santos).
• Report error with -sup when target tree is not as "rooted/unrooted" as tree set (reported by Christian Rinke).
• Crash with multi-threading (-nt option) in Windows due to Clang compiler flag (reported by Wo Niu and others).

Bugfixes:

• Crash with -wbt option for non-reversible models (reported by Suha Naser).

New features:

• New model +ASC_MIS for ascertainment bias correction with missing data (joint work with Mark Holder).
• New model +ASC_INF for ascertainment bias correction with parsimony information sites only (joint work with Mark Holder).

• New option --symtest to perform the maximum tests of symmetry, marginal symmetry and internal symmetry (MaxSymTest).

Important changes:

• Amino-acid frequencies of DAYHOFF, DCMUT, JTT, MTREV, WAG, CPREV, LG, MTZOA, PMB, JTTDCMUT, FLU are modified with higher precision and normalised to 1 (thanks Ben Redelings). This may lead to tiny change in log-likelihood (i.e. from 3 digit after comma) but does not affect +F model.

New features:

• Support '.' syntax for alignment length in partition file (requested by Teofil Nakov).

Bugfixes:

• Crash with -bnni option and GENE/GENESITE resampling (reported by Emmanuel Cantu).
• Incorrect WARNING about bootstrap convergence with -bnni option (reported by Max_IT).
• Numerical issue with likelihood scaling for gcc under -O3 optimisation.
• Handling fixed substitution rates (reported by @bbuchfink).

Bugfixes:

• Partition models with non-reversible models.
• Various issues with --model-joint option.

Bugfixes:

• Crash with joint model in edge-linked partition model (--model-joint with -spp).
• Properly computing degree of freedom for linked model.
• Return reduced memory requirement for ModelFinder.
• IMPORTANT: Numerical issue with Eigen3 decomposition when some state frequency is nearly zero.
• IMPORTANT: Thread-safe issue with --model-joint.

New options:

• --out-alignment will print partition file if applicable (requested by Marianne Espeland).

New features:

• Checkpoint time interval is automatically increased if dumping time takes > 5% of the interval.
• For edge-unlinked partition model (-sp) partition trees with unlinked branch lengths will be printed to .parttrees file (requested by Stephen Crotty).
• Better handling zero state_freq for nonrev models.
• Allow to compile OpenMP version with apple-clang (at least Mac OS High Sierra 10.13).
• Make boost library required by default.
• Fix problem GTR20+FO optimisation.
• Zlib compression level is changed from 9 to 1 for speed.
• New option --df-tree to print tree for gDF1 into cf.stat file (requested by Dan Vanderpool).
• New option --root-test to test all possible rooting of the final tree.

Bugfixes:

• Crash with edge-unlinked model (-sp) and -bnni option (reported by Mark Miller).

New options:

• --maxsymtest to perform maximum test of symmetry.

Bugfixes:

• ASSERT on symmetry of Q (reported by Bradley Martin).