Assets 2

Addresses a bug in the specification of +G+I models.

@sjspielman sjspielman released this Apr 12, 2018 · 2 commits to master since this release

Assets 2

Inclusion of six additional protein models: HIVW, HIVB, mtMet, mtInv, mtVer, gcpREV.

@sjspielman sjspielman released this Dec 18, 2017 · 3 commits to master since this release

Assets 2

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

@sjspielman sjspielman released this Oct 12, 2017 · 4 commits to master since this release

Assets 2

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.

@sjspielman sjspielman released this Jul 24, 2017 · 5 commits to master since this release

Assets 2

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

@sjspielman sjspielman released this Jan 10, 2017 · 9 commits to master since this release

Assets 2

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

@sjspielman sjspielman released this Dec 16, 2016 · 10 commits to master since this release

Assets 2

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.

@sjspielman sjspielman released this May 18, 2016 · 15 commits to master since this release

Assets 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.

@sjspielman sjspielman released this May 15, 2016 · 16 commits to master since this release

Assets 2

Fixed small typo and updated README.

@sjspielman sjspielman released this May 15, 2016 · 20 commits to master since this release

Assets 2

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