---
name: "proalign"
section: "1"
platform: "linux"
package: "proalign"
version: "0.603-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/proalign"
---

# proalign(1)

a probabilistic multiple alignment 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