Pyvolve v0.8.7

Adds JC69 (equal rates) model of amino acid evolution.

Pyvolve v0.8.6

Updates to Evolver class to tabulate a matrix substitution counts (assumes single changes only!) for a simulation.
This matrix can be exported with the argument countfile = file.txt when calling an Evolver class.

Pyvolve v0.8.5

Updated to force a numpy random seed reset for each call to Evolver.

Pyvolve v.0.8.4

Addresses a bug in v0.8.3 where newick tree parser threw an error when encountering a user-labeled root.

Pyvolve v0.8.3

Fixed a bug where scale_tree in the newick.py module was not applied for user-named internal nodes.
Additionally removed underscore from default internal node names (now internalNodeX instead of internal_nodeX) because underscore can occasionally prevent proper parsing due to model flag interference.

Pyvolve v0.8.2

Two primary updates:

1. Custom models can now be provided with custom state frequencies. To provide custom state frequencies, the provided matrix must be symmetric. Under any circumstance, the rows of the matrix should sum to 0 (whether frequencies are provided or not!)
2. Codon models (GY, MG) can now be scaled such that branch lengths indicate the mean number of neutral substitutions per unit time. To invoke, include the argument: neutral_scaling=True when defining a Model object, for example:
   m = Model("GY", {"omega":0.4}, neutral_scaling=True.

Pyvolve v0.8.1

Fixed small typo and updated README.

Pyvolve v0.8

Resolved Python3 incompatibility issue. Pyvolve is now fully functional for both Python2 and Python3.

Pyvolve v0.7.6

Added argument for both the newick and evolver modules. This argument scales the entire tree (i.e. all branch lengths) with a given multiplier. Note that it is provided in both modules for different general purposes: In newick, it scales tree for all future use. In Evolver, it scales tree only for this particular simulation, so it's useful for replicates each of which have a different scaling factor.

Pyvolve v0.7.5

Updated model flag specification in phylogeny, as requested by I. Davydov. Can now provide model flag names with hashtags or underscores.
By providing leading and trailing symbols, e.g. #modelflag# or modelflag, the model flag is propagated to all descendants.
Else, if only a leading underscore, e.g. #modelflag or _modelflag, the model is NOT propagated to descendants and hence applies only to that branch.