Javamony

Based on the not-so-successful Pysimony (https://sourceforge.net/projects/pysimony/), the same determined student takes another go at the phylogenetic problem.

Javamony is invoked as follows:
java -jar Javamony.jar [input.fasta] [random / stepwise (starting tree)] [# of bootstraps] [outgroup taxon #1] [outgroup taxon #2] ...

Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve fundamental problems in phylogenetics. Therefore, for my own educational benefit, all code is original. Of course, there are probably a good deal of mistakes as well.

I distribute Javamony, as I did Pysimony, hoping that it will be of educational value to someone else or at least vaguely amusing.

Upcoming features will be:
- Support for Amino Acid sequences
- Support for additional file formats (e.g. Nexus)
- Multithreading
- Additional scoring methods (e.g. maximum likelihood)