hhalign(1) on Linux
The text 1ec34fd79178, as Debian 7 (Wheezy) shipped it.
align a query alignment/HMM to a template alignment/HMM
Flags it lists
-
-Aa3m -
-B -
-E -
-M -
-Oa3m -
-P -
-Z -
-aliw -
-alt -
-atab -
-b -
-calm -
-corr -
-cov -
-cslib -
-dali -
-def -
-diff -
-dmap -
-dsca -
-dthr -
-dwin -
-egq -
-egt -
-gapb -
-gapd -
-gape -
-gapf -
-gapg -
-gaph -
-gapi -
-i -
-id -
-mac -
-mact -
-nocons -
-nocontxt -
-nodssp -
-nopred -
-norealign -
-o -
-ofas -
-p -
-pca -
-pcb -
-pcc -
-pcm -
-png -
-pre_pca -
-qid -
-qsc -
-r -
-rank -
-realign -
-sc -
-seq -
-shift -
-ssa -
-ssconf -
-ssm -
-ssw -
-sto -
-t -
-tags -
-tc -
-tct -
-v -
-z