proalign1
A probabilistic multiple alignment program
Usage
proalign [OPTIONS]
Overview
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
Releases
Unchanged in 6 releases since Debian 8 (Jessie).