I'm just wondering if I have reference genomes for 5 species, how to use the EPO pipeline in ensembl to do multiple alignment.
I know I can download the EPO 35 eutherian or EPO 6 primates from ftp, but I still very curious about the 'de novo' multiple alignment pipeline, when I looked through the original EP paper published in GR (Benedict et al. 2008), I know that the Enredo need a set of nonoverlapping GPAs(Genomic Point Anchor) as input file. So I looked the Enredo Genomic Point Anchor Generation section in supplementary, it is very complicated, to derived the GPA, Gerp[Cooper et al., 2005] and BlastZ-net or Lastz-net should be included.
Maybe it's just because I'm a new in multiple alignment and cannot initialize the idea of how to do, what to do when I see the GPAs generation part. Can somebody give me sort of simple pipeline to do 'de novo' multiple genome alignment from reference genomes of several species to MSA output?
Thanks in advance