Pyvolve v0.6.1

This minor update allows users to provide a root sequence (MRCA) to a partition. Use the key "root_sequence" when defining a Partition object. In this circumstance, the "size" argument may be omitted.

Pyvolve v0.6

Updates:

1. Gamma + Pinv rate heterogeneity explicitly incorporated.
2. Addressed issue in which, under certain conditions, rate categories were not properly assigned in proportion to their probabilities. Note that pyvolve now requires numpy >= 1.7, which is now indicated in setup.py.

Pyvolve v0.5.2

Users can now specify node names in newick phylogeny. Node names must begin with a letter and cannot contain colons.

Pyvolve v0.5.1

Updated newick parser to give more informative error messages and instructions when branch lengths are missing.

Pyvolve v0.5

Minor updates to mutation-selection model construction.

Pyvolve v0.4

Minor updates. Now includes the AB model of antibody amino-acid evolution.

Pyvolve v0.3

Minor bug fixes.
This release includes new amino acid models mtMam, mtREV24, and DAYHOFF.
Example scripts in examples/ directory have now all been written.

Pyvolve v0.2

Pyvolve now includes the ability for users to specify a custom "code" (e.g. states) when providing a custom rate matrix. For example, one could provide a custom 3x3 rate matrix and specify that Pyvolve evolve states "0", "1", "2". This option may be useful for simulating character evolution until a more formal framework is available.