v3.4

Multithreading of recombination detection and gap inference.

v3.3.5

• Update installation instructions

v3.3.4

• Fixes installation problems
• Allows for input files with spaces in their names

v3.3.3

Error with previous version tag - no change to code.

v3.3.2

Enable seed setting and minor fixes.

Gubbins v3.3.1

Added plotting capability

v3.3.0

Updates the scripts for input alignment generation and plotting script.

v3.3

Adds in the ability to use IQtree for model selection, use of IQtree fast mode, and IQtree+LSD for generating time-calibrated trees. Additional improvements to model handling (using different models for tree construction and base substitution reconstruction), input parsing and testing.

v3.2.1

Version 3.2.1 - improved and more flexible detection of small recombinations

Version 3.2

Upgrades to the memory efficiency and speed of the joint ancestral reconstruction.