TaxonDNA: Extensible Bioinformatics in Java
Both SpeciesIdentifier and SequenceMatrix are distributed as Java Archive (JAR) files, requiring Java 1.4.2 or higher to work. If you have a Windows more recent than Windows XP or MacOS X more recent than Tiger or above, you should be good to go.
Getting it working
Please download the releases from the links mentioned above. On most recent operating systems, you'll be able to double-click on the enclosed JAR file to start the program immediately. If you're on Windows, please use the batch file: it'll give Java additional memory to run the program with.
All releases come with a README file which should help you get started. If you have any problems, please get in touch with me for any help.
You can get the complete source code for TaxonDNA from our GitHub repository.
Some programs which work well with TaxonDNA include:
AlignmentHelper (you will need to scroll to the bottom of the page). AlignmentHelper helps align coding nucleotide sequences by translating them into amino acid sequences, aligning them in Clustal or Muscle, and then translating them back into amino acid sequences.