Decrease Redundancy
This program allows you to reduce the redundancy in a set of aligned or unaligned sequences.
The algorithm used by this program was developed by Cédric Notredame and is unpublished.
The algorithm used by this program was developed by Cédric Notredame and is unpublished.
The trim algorithm works as follow:
- Computes all the pairwise alignments (PAM250, gop=-10, gep=-1) or use a multiple alignment.
- Measure the \%id (number id/number matches) of each pair
- if a minimum identity min% is set: all the sequences with less than min% identity with ANY sequence in the set will be removed so that in the remaining set ALL the pairs of sequences have more than min% identity. The removal will stop uncompleted if the set becomes smaller than n.
- Remove one of the two closest sequences until either n is reached or until all the sequences have less than max% identity.
- return the new set.