I am trying to annotate the genome of a recently-sequenced primate species. I noticed that the UCSC browser folks have performed a 46-species whole-genome multiple alignment based on hg19, and I'd like to take advantage of that rather than starting a multi-species genome alignment from scratch. Is there a way for me to take my species' genome and align it into the existing 46-species alignment without restarting the whole thing? I am prepared to accept that the result may not be identical to what I would get if I started from scratch. Essentially my input is a set of MAF files (one for each human chromosome) and a fasta file of all the chromosomes and unlocalized scaffolds in my primate species.