Distance-based methods

NINJA is a great neighbor joining program that is fast and feature full. It is developed by Travis Wheeler and can be found here.

Download and Compilation

From the website listed above, you can download the program. It is a java program and so it doesn’t require compilation. Inside the folder is a Ninja.jar file and a ninja file. That is all you need.

Running NINJA

To run ninja, you will just need to run


If you did that, you will see a bunch of errors. If you try

./ninja --help

NINJA takes an aligned fasta file and can be run like this

./ninja file.aln > outfile.tre

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