To many gaps in motifs done by GLAM2

[renewiegandt]

With huge clusters GLAM2 has problems finding motifs without (too) many gaps.

A possible solution are the following parameters which can be set:

Tuning deletion and insertion preferences
Use -D and -E to tune deletion preferences, and use -I and -J to tune insertion preferences. The relative values of -D and -E control glam2's aversion to deletions: increasing -E relative to -D makes it more averse. Likewise, increasing -J relative to -I makes glam2 more averse to insertions. The absolute values of -D and -E control how much glam2 prefers deletions to occur at the same (fragile) positions: if -D and -E are both low, it strongly prefers deletions to occur at the same positions, otherwise not. Likewise, if -I and -J are both low, it strongly prefers insertions to occur at the same positions. To turn off deletions and insertions completely, set -E and -J to huge values:

glam2 -E 1e99 -J 1e99 n my_nucs.fa

By setting the -E and -J Parameter higher it could/should solve the problem.