What is Morphy?
Morphy is a free, open-source tool for phylogenetic analysis of discrete character data. The program's main unique feature is the ability to recognize gap symbols as an inapplicable value instead of treating it as missing data. This generates logically correct ancestral state sequences during tree length counting and searches. However there are differences in the method of tree length counting that reduce the amount of redundant information and consequent biases.The algorithm is described in our paper here.
Morphy is written by Martin Brazeau and Chris Desjardins. The algorithms for handling inapplicable characters use a fast, but approximate method similar to that developed by Jan De Laet (2005, 2015). but were developed for implementation by Martin Brazeau, Thomas Guillerme, and Martin R Smith.
Obtaining all the source
Morphy is undergoing major changes and a wholesale re-write under the hood. It will be much faster and more functional for realistic datasets. The old libraries (with the exception of the user interface) will all be replaced by a new unified library. Anyone wishing to contribute to this project is welcome to get in contact.