Description of feature
In pipesnake v.1.2, users are only able to trim initial MAFFT alignments with GBlocks which is sometimes too aggressive. Shorter sequences like UCEs that have variable flanking regions may be trimmed by GBlocks such that they do not contain variable sites.
Another trimming software that could be incorporated in pipesnake is ClipKit. I've tried trimming with ClipKit and it seems to yield higher quality alignments.
Additionally, some users may be interested in using TAPER to 'correct' their alignments after trimming.
Description of feature
In
pipesnakev.1.2, users are only able to trim initial MAFFT alignments withGBlockswhich is sometimes too aggressive. Shorter sequences like UCEs that have variable flanking regions may be trimmed byGBlockssuch that they do not contain variable sites.Another trimming software that could be incorporated in
pipesnakeis ClipKit. I've tried trimming with ClipKit and it seems to yield higher quality alignments.Additionally, some users may be interested in using TAPER to 'correct' their alignments after trimming.