[Genome] MAF alignments - non-orthologous regions

[Daniel Gaffney]

Hi there,
I have a quick question on the availability of non-orthologous sequence 
in 17 vertebrate species MAF alignments. Do the MAF alignments include 
all sequence currently available for each of the constituent species? 
i.e. is lineage specific sequence that apparently has no orthologue 
anywhere else in the vertebrate phylogeny still included (presumably 
aligned with gaps in the other 16 species)? Or is the only sequence in 
the alignments that which can be aligned to at least one other 
vertebrate species?
Cheers
Dan

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Daniel Gaffney		          

McGill University and Genome Quebec Innovation Centre
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