Joseph W. Brown

I do not understand the problem. Why were the results incorrect? What were the results? What are the expected results? What was the command you used? Also, the upload of...

I'm sorry but I still do not understand what went wrong. What is wrong with the gene2 results? What were they? What were you expecting? What command did you use?

This is what I get when I examine your files: Gene1 (original): ``` josephwb@Potiphar-Breen:issue$ pxlssq -s gene1_trimAl.txt File type: fasta Number of sequences: 84 Is aligned: true Sequence length: 1086...

I note that gene2_trimAl.txt seems to have Windows line breaks: ``` josephwb@Potiphar-Breen:issue$ file gene1_trimAl.txt gene1_trimAl.txt: ASCII text, with very long lines josephwb@Potiphar-Breen:issue$ file gene2_trimAl.txt gene2_trimAl.txt: ASCII text, with very long...

You can also run Gene2 through `pxlssq`; if it fails there, it is almost certainly the line breaks: ``` pxlssq -s gene2_trimAl.txt ```

Do you have some example input and output? `pxcolt` can collapse _nodes_, but you want to flag _trees_, yes?

I understand, but could you please provide example input files?

Those programs were [purposefully removed from the default build](fd445c32b9b77d47a5153e7111341f5b4a88b8a5) because they are meant more for instruction than publication-worthy analysis. These may be removed entirely. I am looking at your other...

Ok I will get to this later today. Thanks for the help.

Hey @nileshpatra. I did not draft the original makefile. It _seems_ to me that the `OPT_FLAGS` we use is standing in for `CXXFLAGS`. Would it work for you if I...