@bqminh bqminh released this Oct 29, 2018 · 4 commits to master since this release

Assets 8

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.

@bqminh bqminh released this Oct 28, 2018 · 4 commits to master since this release

Assets 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".

@bqminh bqminh released this Oct 23, 2018 · 8 commits to master since this release

Assets 8
  • 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).
Pre-release

@bqminh bqminh released this Oct 23, 2018 · 7 commits to master since this release

Assets 8

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).

@bqminh bqminh released this Oct 8, 2018 · 13 commits to master since this release

Assets 8
  • 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.

@bqminh bqminh released this Sep 28, 2018 · 13 commits to master since this release

Assets 5

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).
Pre-release

@bqminh bqminh released this Sep 12, 2018 · 14 commits to master since this release

Assets 4

Notable features:

  • -spu PARTITION_FILE to perform separate phylogenetic analysis for each partition.
  • NONREV for general non-reversible models.
  • --symtest to perform Symmetry Test as of Jermiin et al.
  • --terrace to check if ML tree lies on a phylogenetic terrace (code from https://github.com/terraphast)
  • --tbe to perform transfer bootstrap expectation (code from https://github.com/evolbioinfo/booster)

New options:

  • -sup2 to map support values from a set of trees with unequal taxon sets onto a target tree.
  • -rf2 to compute Robinson-Foulds distance between two sets of trees with unequal taxon sets.
  • --link-model to link substitution models across partitions.
  • --root-move-dist to optimise rooting position up to a certain distance (default: 2).
  • --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.
  • --symtest-remove-bad to do --symtest and remove bad partitions.

@bqminh bqminh released this Sep 6, 2018 · 15 commits to master since this release

Assets 8
  • Show more precision in log likelihood with --show-lh (thanks Benjamin Redelings)
  • Reimplement -tina and -st MULTI option (requested by Ingo Ebersberger)

Bugfixes:

  • Crash at the end with --runs and partition model (reported by David Maddison)

@bqminh bqminh released this Aug 23, 2018 · 22 commits to master since this release

Assets 8

Important changes:

  • Temporarily disable AU test due to unresolved numerical issue when bp-rell are all zeros.

Bugfixes:

  • Checkpointing issue in ModelFinder for mixture models causing incorrect likelihoods with e.g. -madd C10 (reported by Juergen Strassert).
  • Checkpointing Lie Markov models.
  • (v1.6.6) Incomplete parsing of site positions of partition file (reported by Alexey Kozlov).
  • Parsing polymorphic states from NEXUS file (reported by Steven Heritage).
  • Use of only 1 thread when #partitions < #cores (reported by Alexey Kozlov).
  • Double RAM usage for -bnni option (reported by Juergen Strassert).
  • Over-bound for optimizeTreeLengthScaling causing too long branch lengths in extreme cases (reported by vikaszsi77).
  • Exclude ORDERED model by default for morphological data due to frequent numerical underflow.
  • (v1.6) -m ..MERGE.. wrong concatenateAlignments with missing data (reported by David Dunchene).
  • Error message instead of crash when using -bsam with non-partition model (reported by Sarah Jensen).