This script aims to "cull" redundant alignments. It removes alignments whose coordinates in the top-most sequence are contained in LIMIT or more higher-scoring alignments.
Alignments using opposite strands of the top-most sequence are not considered to contain each other.
The alignments must have been sorted beforehand by maf-sort. If not, maf-cull will quit with an error message.
You can use it like this:
maf-cull --limit=3 sorted-alignments.maf > culled.maf maf-cull -l3 sorted-alignments.maf > culled.maf
If you want to cull based on a sequence other than the top one, use maf-swap to bring that sequence to the top.
This type of culling can also be done by NCBI BLAST, and it is described in this article:
Winnowing sequences from a database search. Berman P, Zhang Z, Wolf YI, Koonin EV, Miller W. J Comput Biol. 2000 7:293-302.
-h, --help Print a help message and exit. -l LIMIT, --limit=LIMIT Set the culling limit to LIMIT.