This is the command proalign that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Use proalign online using onworks.net services
