NAME

       proalign - a probabilistic multiple alignment program

SYNOPSIS

       proalign [OPTIONS]

DESCRIPTION

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

OPTIONS

       -nogui force command line

       -seqfile=<sequence file>

       -treefile=<tree file>

       -newtree
              compute a new guide tree

       -sample
              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

       -nocorrection
              no correction for pairwise distances on guide tree computation

       -notrailing
              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

       -writemean
              write mean posterior probability of sites

       -writeall
              write posterior probability of each node

       -writeroot
              write root node character probabilities

       -wag   use WAG probability table

       -dayhoff
              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