blast2malign is a perl script that creates a multiple alignment
(relative to the query) from the database hits of a BLAST search.
Insertions in the database sequences are not represented in the
output.

It is intended to be a quick and easy to use method for getting a
fairly accurate multiple alignment for initial phylogenetic or other
analyses.

The script attempts to determine if HSPs for a particular database
sequence correspond to the same or to different genes and groups HSPs
into multiple gene groups if possible and represents them as separate
sequences in the mutiple alignment. HSPs corresponding to a particular
gene group are combined into a single sequence. If two HSPs from the
same group hit the same region of the query sequence the HSP with the
highest average sequence identity has priority.

type "perldoc blast2malign" for some other documentation
