hhsearch(1) on Linux
The text cbb7afa1e7c4, as Debian 7 (Wheezy) shipped it.
search a database of HMMs with a query alignment or query HMM
Flags it lists
-
-B -
-E -
-M -
-Ofas -
-Z -
-aliw -
-alt -
-b -
-cons -
-corr -
-cov -
-cpu -
-csb -
-cslib -
-csw -
-d -
-dbstrlen -
-diff -
-e -
-egq -
-egt -
-excl -
-forward -
-gapb -
-gapd -
-gape -
-gapf -
-gapg -
-gaph -
-gapi -
-i -
-id -
-mac -
-mact -
-maxres -
-neff -
-nocons -
-nocontxt -
-nodssp -
-nopred -
-norealign -
-o -
-oa3m -
-p -
-pca -
-pcb -
-pcc -
-pcm -
-qid -
-qsc -
-sc -
-seq -
-shift -
-ssa -
-ssconf -
-ssm -
-ssw -
-tags -
-v -
-vit -
-z