jalview1

Usage

Overview

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