proalign: A probabilistic multiple alignment program

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