proalign - a probabilistic multiple alignment program

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

       proalign - a probabilistic multiple alignment program

-nogui force command line

       -seqfile=<sequencefile>-treefile=<treefile>-newtree
              compute a new guide tree

       -sample
              sample traceback path; if not given, Viterbi is chosen

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

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

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

       -gapprob=<gapsubstitutionprobability>
              if not given, default is used

       -bwidth=<searchbandwidth>
              if not given, default is used

       -distscale=<distancescalefactor>
              for branch lengths

       -nocorrection
              no correction for pairwise distances on guide tree computation

       -notrailing
              no trailing sequence corrcection

       -trailing=<trailingsequencecorrectionlength>
              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=<alignmentfile>-outformat=pir,-outformat=msf,-outformat=phylip,or-outformat=nexus
              output format

       -quiet no log

ProAlign                                            May 2013                                         PROALIGN(1)

proalign[OPTIONS]