Does anyone know if the MAF format have a convention of right or left aligning its gaps/indels as seen in VCF files (where an indel is always left-aligned)?. I generated my own multiple sequence alignment using the multiz pipeline from UCSC and found that in some cases a gap is right aligned, in other cases its left aligned.
What I mean is the following, assume that I have 3 sequences, looking only at the sequence part in the MAF format,
In this case the gap is left aligned, if it was right aligned, I would see the following:
In my MAF formats, I see both instances occurring, which makes me wonder if there is a set convention or not. If there isn't, I would also appreciate any references on tools which can left align these gaps in the sequence file if there are any available.