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. A forthcoming paper will document these algorithms.
Morphy is written by Martin Brazeau and Chris Desjardins. The algorithms for handling inapplicable characters owe credit to the work of Jan De Laet (2005, 2015), but were developed for implementation by Martin Brazeau, Thomas Guillerme, and Martin R Smith.
Obtaining all the source
There is currently no binary executable that can be downloaded as we are still working on a cross-platform build system. Morphy is written in C and C++ distributed as a set of modules/libraries. If you have cmake installed, you can use the Morphy manifest along with repo tool to clone all of the Morphy project modules and other dependencies. A python script in the build directly will run a cmake build system to compile an executable for your machine. There is, unfortunately, very little that Morphy will actually do for you at this time.