TBA - work with multiple alignment MAF format

The resulting TBA multiple alignment is now ready for analysis. Several tools (in addition
to the above mentioned maf project) are available to aid you in this process and are
described in the README. Several are worth noting here:

maf order orders the species in each alignment block to some speci ed order. It will also
remove unwanted species from the multiple alignment (rather than rerunning tba
with a subset of species).
mafFind extracts a sub-region of the multiple alignment.
maf2fasta takes a projected MAF le and re-formats it to either MultiPipMaker format or
multi-FASTA format, representing the entire reference species' sequence, but only
5the alignable portions of all other species' sequences. This program is particularly
useful since the MAF speci cation is relatively new
(see http://genome.ucsc.edu/goldenPath/help/maf.html)
and is not yet as universal as the FASTA format.

http://www.bx.psu.edu/miller_lab/