Scroll to navigation

JALVIEW(1) General Commands Manual JALVIEW(1)

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

Run Jalview without User Interface.
Use the given Jalview properties file instead of users default.
The colourscheme to be applied to the alignment
Add precalculated annotations to the alignment.
Load the given newick format tree file onto the alignment
Use the given file to mark features on the alignment.
Create alignment file FILE in Fasta format.
Create alignment file FILE in Clustal format.
Create alignment file FILE in PFAM format.
Create alignment file FILE in MSF format.
Create alignment file FILE in Pileup format
Create alignment file FILE in PIR format.
Create alignment file FILE in BLC format.
Create alignment file FILE in JSON format.
Create alignment file FILE in Jalview format.
Create PNG image FILE from alignment.
Create SVG image FILE from alignment.
Create HTML file from alignment.
Create BioJS MSA Viewer HTML file from alignment.
Create HTML file FILE with image map of PNG image.
Create EPS file FILE from alignment.
Queries the given URL for information about any Jalview user questionnaires.
Turn off questionnaire check.
Turn off check for Jalview news.
Disable the automatic download of templates in the Github repository.
Enable or disable sorting of the given alignment by the given tree
Specify URL for Jabaws services (e.g. for a local installation).
Query nickname for features for the alignments and display them.
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).
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.
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.

SEE ALSO

https://www.jalview.org

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.

06-02-2021