Version 2.2.5

Fixed the issue of reading a tree file with bootstrapping values.

Version 2.2.4

Support exclamation marks in alignments. All exclamation marks will be regarded as gaps.

Version 2.2.3

• New features in AliSim: Users can pre-define mutations that occur along the tree. For more details, please see User Manual.
• Minor bugs fixed.

Version 2.2.2.9

• Fixed the issue of program termination due to numeric overflow even the option --safe is used.
• clean up modelfinder output #14

Version 2.2.2.8

Fixed the greedy algorithm for computing the best-fit partitioning scheme (i.e. option: --merge greedy).

Version 2.2.2.7

Change --scfl option behaviour to ignore sites where at least one subtree shows all gaps/ambiguity for all taxa below that subtree.
The previous sCFL can still be called via -scflg.

Version 2.2.2.6

Fix crash with -wpl option and compile error on mac 13.3

v2.2.2.5

An issue was fixed when the input data set with partitions of multiple data types.

v2.2.2.4

Bugs fixed in AliSim:

• Avoid setting identical random seed numbers when simulating multiple sequence alignments.
• Avoid randomly generating state frequencies when using branch-specific models with equal state frequencies.

v2.2.2.3

Bug fixed:

• an issue that happened when using the partition model.
• an issue of inconsistencies in the number of constant sites for the data with partitions.