Version 4.1

Features

• Show multiple different consensus alignments in bp-analyze.

Speed

• Don't spend so much time on SPR for large trees.

Fixes

• Fix alignment-consensus --strict=1
• Fix character ranges for 1,2,3rd codon position.
• Fix bp-analyze for Numeric(2) alphabet.
• Fix default alphabet and substitution model for binary data.
• Fix allow scaling move to work on negative values.
• Fix proposed alignments in SPR.

Unstable features

• Allow conditioning on "variable" sites via --smodel=<model>|variable
• Make SPR move work on rooted trees.
• Speed up coalescent tree probability.