seg-suite

The seg suite provides tools for manipulating segments and alignments.

Get the latest version: seg-suite-11.zip

Here are some things you can do with it:

Compose alignments

2-sequence alignment x 2-sequence alignment -> 3-sequence alignment
seg-join ab.seg ac.seg > abc.seg

Intersect segments

segment x segment -> intersection
seg-join x.seg y.seg > intersections.seg

It's the same thing

Segments are single-sequence alignments. So, segment intersection is a special case of alignment composition.

Other manipulations