Pyvolve v0.7.4

Addressed implementation issue with gamma-distributed heterogeneity.

Pyvolve v0.7.3

Documentation updates with instructions for ancestral sequence evolution.
Additional sanity checks on provided model, partition objects to the partition, evolver modules, respectively, with some added flexibility for providing this information.

Pyvolve v0.7.2

Minor bug fix.

Pyvolve v0.7.1

Addressed issue where scaling slightly off for heterogeneous codon models in which the dN/dS categories are not equiprobable.

Pyvolve v0.7

Substantial update to matrix construction, specifically scaling procedure.
All nucleotide, amino-acid, empirical codon, and mechanistic codon model matrices are scaled as usual ("persite") scaling.
Heterogeneous codon model matrices are scaled such that the mean substitution rate for the mean dN/dS across all categories is equal to 1.
Mutation-selection model matrices are scaled such that the mean neutral substitution rate is equal to 1.

Pyvolve v0.6.6

Cleaned up error messages, catching and included formal warning upon use of the 'scale_matrix' keyword argument when defining a Model.

Pyvolve v0.6.5

Minor update changes the Tree class to be called Node, in order to avoid potential conflicts with the DendroPy library, which also has a Tree class. Additionally, both 'scale_matrix' and 'scaling' may be used as keyword arguments when defining a Model object to involve neutral scaling, but eventually 'scale_matrix' will be deprecated. A warning statement will now print out when this argument is given.

Pyvolve v0.6.4

Neutral rate-matrix scaling should now be specified with the keyword argument <scaling="neutral"> when defining a Model object.

Pyvolve v0.6.3

Addressed two issues:

1. Fixed minor bug in helpful_scripts/compute_dnds_from_mutsel.py module where the variable "frequencies" was used rather than "codon_frequencies".
2. Fixed bug in Pyvolve where the neutral scaling was improperly computed when providing fitness values to a MutSel model

Pyvolve v0.6.2

Minor update to include convenience functions to return various parameters from a Model object.