---
name: "jalview"
section: "1"
platform: "linux"
package: "jalview"
version: "2.11.4.1+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/jalview"
---

# jalview(1)

Multiple alignment editor

## NAME

jalview - Multiple alignment editor

## SYNOPSIS

**jalview -open \[*FILE*\] \[*OUTPUT\_FORMAT*\] \[*OUTPUT\_FILE*\]**

## DESCRIPTION

**Jalview** provides facilities for viewing/editing and otherwise manipulating sequence alignments (DNA, amino acids).

## OPTIONS

- **-nodisplay**

  Run **Jalview** without User Interface.

- **-props** FILE

  Use the given **Jalview** properties file instead of users default.

- **-colour** COLOURSCHEME

  The colourscheme to be applied to the alignment

- **-annotations** FILE

  Add precalculated annotations to the alignment.

- **-tree** FILE

  Load the given newick format tree file onto the alignment

- **-features** FILE

  Use the given file to mark features on the alignment.

- **-fasta** FILE

  Create alignment file FILE in Fasta format.

- **-clustal** FILE

  Create alignment file FILE in Clustal format.

- **-pfam** FILE

  Create alignment file FILE in PFAM format.

- **-msf** FILE

  Create alignment file FILE in MSF format.

- **-pileup** FILE

  Create alignment file FILE in Pileup format

- **-pir** FILE

  Create alignment file FILE in PIR format.

- **-blc** FILE

  Create alignment file FILE in BLC format.

- **-json** FILE

  Create alignment file FILE in JSON format.

- **-jalview** FILE

  Create alignment file FILE in **Jalview** format.

- **-png** FILE

  Create PNG image FILE from alignment.

- **-svg** FILE

  Create SVG image FILE from alignment.

- **-html** FILE

  Create HTML file from alignment.

- **-biojsMSA** FILE

  Create BioJS MSA Viewer HTML file from alignment.

- **-imgMap** FILE

  Create HTML file FILE with image map of PNG image.

- **-eps** FILE

  Create EPS file FILE from alignment.

- **-questionnaire** URL

  Queries the given URL for information about any **Jalview** user questionnaires.

- **-noquestionnaire**

  Turn off questionnaire check.

- **-nonews**

  Turn off check for Jalview news.

- **-nohtmltemplates**

  Disable the automatic download of templates in the Github repository.

- **-sortbytree** OR **-nosortbytree**

  Enable or disable sorting of the given alignment by the given tree

- **-jabaws** URL

  Specify URL for Jabaws services (e.g. for a local installation).

- **-fetchfrom** nickname

  Query nickname for features for the alignments and display them.

- **-groovy** FILE

  Execute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN).

- **-jvmmempc=PERCENT**

  Only available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT percents of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.

- **-jvmmemmax=MAXMEMORY**

  Only available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.

- **https://www.jalview.org**

  ## SEE ALSO

## AUTHOR

This manual page was written by Vincent Fourmond \<fourmond@debian.org\> and Pierre Gruet \<pgt@debian.org\> from the Debian project, but may be used by others.