Provided by: proalign_0.603-4_amd64 bug


       proalign - a probabilistic multiple alignment program


       proalign [OPTIONS]


       Only  limited usage of the program is possible from command line.  Better use version with
       GUI (start without OPTIONS).


       -nogui force command line

       -seqfile=<sequence file>

       -treefile=<tree file>

              compute a new guide tree

              sample traceback path; if not given, Viterbi is chosen

       -delta=<HMM delta> or -delta=estimate
              if not given, default is used

       -epsilon=<HMM epsilon> or -epsilon=estimate
              if not given, default is used

       -gapfreq=<gap frequency>
              if not given, default is used

       -gapprob=<gap substitution probability>
              if not given, default is used

       -bwidth=<search band width>
              if not given, default is used

       -distscale=<distance scale factor>
              for branch lengths

              no correction for pairwise distances on guide tree computation

              no trailing sequence corrcection

       -trailing=<trailing sequence correction length>
              for missing ends

       -penalize=true, or =false
              penalize end gaps on pairwise alignments for guide tree

              write mean posterior probability of sites

              write posterior probability of each node

              write root node character probabilities

       -wag   use WAG probability table

              use Dayhoff probability table

       -jtt   use JTT probability table

       -outfile=<alignment file>

       -outformat=pir, -outformat=msf, -outformat=phylip, or -outformat=nexus
              output format

       -quiet no log