maf-cut

maf-cut cuts out parts of MAF format alignments. For example:

maf-cut chr7:1234000-1235000 alignments.maf

This gets alignment parts within the range 1234000-1235000 of the sequence named "chr7".

The ranges are zero-based. For example, chr7:0-1000 means the first 1000 bases of chr7.

You can omit the sequence name:

maf-cut 1234000-1235000 alignments.maf

Then, the range applies to the topmost sequence in each alignment.