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).
- -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