Description of scripts that accompany LAST
==========================================

maf-join
--------

This script joins two or more sets of pairwise (or multiple)
alignments into multiple alignments::

  maf-join aln1.maf aln2.maf aln3.maf > joined.maf

The top genome in each input file should be the same, and the script
simply joins alignment columns that are at the same position in the
top genome.  IMPORTANT LIMITATION: alignment columns with gaps in the
top sequence get joined arbitrarily, and probably wrongly.  Please
disregard such columns in downstream analyses.  Each input file must
have been sorted using maf-sort.  For an example of using LAST and
maf-join, see multiMito.sh in the examples directory.


maf-swap
--------

This script changes the order of the sequences in MAF-format
alignments.  You can use option "-n" to move the "n"th sequence to the
top (it defaults to 2)::

  maf-swap -n3 my-alignments.maf > my-swapped.maf


maf-sort
--------

This sorts MAF-format alignments by sequence name, then strand, then
start position, then end position, of the top sequence.  You can use
option "-n" to sort by the "n"th sequence instead of the top sequence.


Limitations
-----------

1) The scripts that read MAF format work with the simple subset of MAF
   produced by lastal, but they don't necessarily work with more
   complex MAF data from elsewhere.

2) These scripts do not work for DNA-versus-protein alignments:
   last-dotplot, maf-join.
