MafFilter is really useful to parse and filter maf files, and it would be even better if there was a way to use it to assess the reliability of the different alignments.
The files I use do not have any score natively printed for every block and it could be great if MafFilter was able to compute a quality score of the Multiple Sequence Alignments by itself (using methods such as Heads or Tails, G. Landan and D. Graur 2007), so that it would be way easier to filter out the worst alignments.
MafFilter is really useful to parse and filter maf files, and it would be even better if there was a way to use it to assess the reliability of the different alignments.
The files I use do not have any score natively printed for every block and it could be great if MafFilter was able to compute a quality score of the Multiple Sequence Alignments by itself (using methods such as Heads or Tails, G. Landan and D. Graur 2007), so that it would be way easier to filter out the worst alignments.