Running Paircomp Locally

1. Download and compile paircomp locally:

svn co http://svn.idyll.org/repos/cartwheel/trunk/paircomp paircomp
cd paircomp
make depend
make

2. Generate the comparison:

bin/paircomp seq1.fasta seq2.fasta 20 0.7 seq1-seq2.cmp

Here '20' is the windowsize and 0.7 is the threshold to use.

3. Generate the 'sister' format XML file:

scripts/paircomp-to-sister se1.fasta seq2.fasta 20 seq1-seq2.cmp seq1-seq2.xml

where '20' is again the windowsize.

At this point you can use FamilyRelationsII to view the output file, e.g.

/path/to/FRII/build/dir/app/view-sister seq1-seq2.xml