What's Changed

• Opt aa freq by @stephaneguindon in #159
• Changed boundaries for GTR param values by @stephaneguindon in #160

Full Changelog: v3.3.20211231...v3.3.20220408

Full Changelog: v3.3.20211118...v3.3.20211231

Full Changelog: v3.3.20211021...v3.3.20211118

This releases fixes a few minor bugs. The manual also explains how to use the XML interface to implement fancy models of substitution (e.g., CAT-like) applied to single- or multiple-gene data sets.

This release does not pass some of the testiphy tests. The problem is minor : it has to do with the routines used for eigenvalue et eigenvector calculation that, in some cases, seem to fall a tad short in terms of numerical precision. In the future releases I will switch to another technique for this task that applies to symmetric matrices (this technique is described in Numerical Recipes).