Note: This version of the FAQ was written on 5 April 2020 for version 0.2 beta.

Q: Why won’t Morphy read my Nexus file?

There are some issues with Nexus file formatting that can cause read issues. The most common is the missing SYMBOLS command in the CHARACTERS (or DATA) block. While Morphy does not strictly require this item, the program uses the Nexus Class Library to handle input and output. These functions appear to choke on Nexus files without a SYMBOLS command.

Q: Why does the world need another phylogeny program?

Perhaps it doesn’t. Morphy has its own way of encoding discrete data internally, it’s own routines for deriving the score of a tree, and its own methods for accelerating the scoring of trees during searches. There is also a lack of serious parsimony programs available that are open-source and would have allowed me to invade the code and re-write these routines. There would be little hope I could have done this without my own practice at writing and building phylogeny programs. So now the world has Morphy.

Q: Why does Morphy only do parsimony?

Because likelihood calculations are slower and more complicated to program. I hope one day to get there.

Q: How many states can Morphy handle?

Morphy can accommodate characters with up to 31 states plus the inapplicable token.

Q: Does Morphy read TNT files?

At present, no. Please convert to a standard nexus file.

Q: How can I contribute to Morphy?

There are several ways to contribute to this project. You can submit bug reports when you encounter any issues. If you are a C or C++ developer, please get in touch about working on the project.

Q: Why can’t Morphy do X?

Morphy is an immature program. There might be a plan to add that feature at some point in the future. If you’d like to see this feature added to Morphy, please contact the developers or submit a feature request.

Q: Why is the Morphy ‘business library’ written in C while the user interface is written in C++?

The mpl library was written by Martin Brazeau who is most comfortable with the C language. The NUI interface for Morphy was mostly written by Chris Desjardins, who is a real programmer. He is smart and uses modern languages like C++. Probably one day the mpl will be re-written in C++.