There are 7 different input/output file types for this software. I will refer them with their default name: tree.txt, tree.bin,, matrx.txt, dist.txt, nhdist.txt, seq.txt. For examples of these files you can check the samples.
I describe the syntax of the text files briefly.
   matrix.txt:    dist.txt, nhdist.txt    seq.txt   tree.txt  
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