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

last-dotplot
------------

This script makes a dotplot, a.k.a. Oxford Grid, of pair-wise
alignments in MAF or LAST tabular format.  It requires the Python
Imaging Library to be installed.  To get a usage message::

  last-dotplot --help

To make a png-format dotplot of alignments in a file called "al"::

  last-dotplot al al.png

To get a nicer font, try something like::

  last-dotplot -f /usr/share/fonts/truetype/freefont/FreeSans.ttf al al.png

If the fonts are located somewhere different on your computer, change
this as appropriate.  To turn off the text and margins completely::

  last-dotplot -s0 al al.png

To limit the plot to 500x500 pixels::

  last-dotplot -x500 -y500 al al.png

If there are too many chromosomes, the dotplot will be very cluttered,
or the script might give up with an error message.  So you may want to
remove alignments involving fragmentary chromosomes first.  For
example, you could use "grep -v" to remove alignments involving
chromosomes with names like "chr1_random"::

  grep -v 'random' al > plotme
  last-dotplot plotme plotme.png


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.