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.