hhmake(1) on Linux
The text 46ce558d437d, as Debian 9 (Stretch) shipped it.
build an HMM from an input alignment or convert between HMMER format and HHsearch format
Flags it lists
-
-M -
-a -
-cons -
-cov -
-diff -
-i -
-id -
-maxres -
-name -
-neff -
-nocontxt -
-o -
-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 -
-seq -
-v