[Genome] galaxy alignments...

[JONATHAN COOPER]

Hi there,
   
  I have been using galaxy to generate multi-alignments (hg17,panTro1,rN3, mM5) from sequence coordinates. Whilst this is v. quick & simple for me (since i have around 1300 sites) I have recently discovered that some of the alignments returned are quite poor, ie some  true homologs are not identified and returned in the alignment. In some cases, 100% panTro1 homologs are left out of alignment results. My question is "are there any other high-throughput methods you know of using ucsc directly?"...I'm guessing the extra level of complexity using galaxy is responsible for some of these inaccuracies...
   
  Any suggestions gratefully received...
   
  Best Regards,
  Jonathan Cooper