PhyML -- Phylogenetic estimation using (Maximum) Likelihood
Full Changelog: https://github.com/stephaneguindon/phyml/compare/v3.3.20211231...v3.3.20220408
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).