Lower tri

[schultzm]

Hi @tseemann

This pull request aims to provide the feature request in issue #33.

The main changes are:

• added a -p option to output the matrix in phylip format
• when -p is on
  • the number of seqs is printed in the top left corner, completing the phylip format
  • instead of i on line 164 in the original code going up to < N, i now goes to <= j, so only the lower triangle and diagonal is printed to stdout.
• added a dummy expected output file in tests/good_phylip.res
• updated the readme

I have tested it on real data and it worked for me as expected, with the output file parseable by quicktree. I haven't added a test to .travis.yaml as I wasn't sure how you were going to implement the tests.

Cheers,

[kloetzl]

Hi Mark,

I left a few comments on your code. Personally, I would be happy to see a phylip-style matrix. However, I would prefer a full matrix. Some tools expect that; and converting a full matrix to a lower-only is much easier than the other way round. (Parsing the lower-only phylip format is surprisingly hard.)

Thanks for your contribution, Fabian