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).