Version 1
Usage:
multiple_sequence_alignment-new-linux.pl -species -chrom -startPos -endPos
opts:
-species Species
-chrom Chrom
-startPos Start position of alignment
-endPos End position of alignment
  -A | Alignment database |
multiple genomic alignment data sets  from UCSC Genome Browse |
  -C | Chrom |
the chromosome |
  -SP | Start position of alignment |
start position of alignment |
  -EP | End position of alignment |
end position of alignment |
  -Q | Query species |
the name of query species |