Version 3.1.6

Improve sequence reconstruction and test for consistency with previous versions.

Version 3.1.5

Merge pull request #328 from nickjcroucher/c_mem

Improvements to reconstruction algorithm

Version 3.1.4

New implementation of JAR and fixes to phylogenetic pipelines.

Version 3.1.3

Transfers SH outputs to final tree

Version 3.1.2

Installs scripts for users, corrects documentation and enables parallel use of a single alignment.

Version 3.1.1

This release improves the accuracy of trees inferred with RAxML-NG.

Version 3.1.0

• Adds scripts for generating inputs and processing outputs
• More thorough checking of tree topology when passing information between methods
• More detailed error handling for incorrect input alignments

Version 3.0.0

Major changes:

• Integrate pyjar
• Integrate RapidNJ
• Enable IQtree as alternative treebuilder
• Enable RAxML-NG as alternative treebuilder
• Enable Fasttree use with ASR
• Enable star phylogenies
• More flexibility in choice of initial tree
• Enable pairwise comparisons
• Log methods for reproducibility
• Migrate CI to GitHub actions

Memory leakage fixes

• fix some memory leakage issues in the main Gubbins code
• add debuggers to Dockerfile

Dockerfile to include gdb

Merge pull request #269 from puethe/gdb

adding gdb to Dockerfile