Morphy 0.5b

Bug fixes

• Fixed counting and displaying of parsimony uninformative and invariant characters

Morphy v 0.4 beta

Release notes:

• Users should experience some (possibly modest) speed improvements over v 0.3b. Search functions now use an internal additive binary representation for ordering characters which simplifies a lot of the internal business logic and restores functionality of some key program optimisations.

Bug fixes:

• None.

Beta release 0.3

See here for instructions on how to use Morphy.

These are continually changing test versions and the software's optimisation routines are undergoing heavy testing and refinement. These versions are meant for testing and providing feedback. Calculation errors are possible. Please report any bugs, errors, or crashes along with detailed steps on how to reproduce the problem in the Issues page.

Release notes:

Users may note slower performance in this release. With the addition of support for ordered characters, I removed a scoring shortcut to avoid unpredictable behaviour. These will be restored in a forthcoming release.

• Reports number of uninformative characters (assumes gap as inapplicable)
• Reports current random number seed at start of heuristic search.
• Accepts input trees from Nexus file.
• Report score(s) of any trees in memory
• Wagner (ordered) parsimony (experimental)
• Internal storage of trees now handled as a dynamic linked list.

Bug fixes:

• File save checks for pre-existing files of same name
• Fixed bug causing the tree buffer to get wiped if the last iteration of the ratchet landed on a suboptimal tree for that rep.
• Fixed bug that would sometimes save suboptimal trees during ratchet searches.

Beta release 0.2

See here for instructions on how to use Morphy.

A note on using this program and publishing results: You do so at your own risk. I make no guarantees of accuracy. These are continually changing test versions and the software's optimisation routines are undergoing heavy testing and refinement. These versions are meant for testing and providing feedback. Calculation errors are possible. If you decide to publish results, then please see the link above for current info on citations. Subject to updates.

Release notes

• Fixed bug causing failed assertion if only one character had 'informative' inapplicable data.
• Fixed input bugs that allowed the program to continue after data reading failed.
• Fixed issue with using open= command on full path to file.