hhsearch(1) on Linux
The text daf895b48d10, as Debian 12 (Bookworm) shipped it.
search a database of HMMs with a query alignment or query HMM
Flags it lists
-
-B -
-E -
-M -
-Ofas -
-Z -
-add_cons -
-aliw -
-all -
-alt -
-atab -
-b -
-corr -
-cov -
-cpu -
-csb -
-csw -
-d -
-diff -
-e -
-egq -
-egt -
-excl -
-gapb -
-gapd -
-gape -
-gapf -
-gapg -
-gaph -
-gapi -
-hide_cons -
-hide_dssp -
-hide_pred -
-i -
-id -
-mact -
-mark -
-maxres -
-maxseq -
-neff -
-nocontxt -
-norealign -
-o -
-oa3m -
-ohhm -
-opsi -
-ovlp -
-p -
-pc_hhm_contxt_a -
-pc_hhm_contxt_b -
-pc_hhm_contxt_c -
-pc_hhm_contxt_mode -
-pc_hhm_nocontxt_a -
-pc_hhm_nocontxt_b -
-pc_hhm_nocontxt_c -
-pc_hhm_nocontxt_mode -
-qid -
-qsc -
-realign -
-realign_max -
-sc -
-seq -
-shift -
-show_ssconf -
-smin -
-ssa -
-ssm -
-ssw -
-v -
-wg -
-z