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