Provided by: jalview_2.11.3.1+dfsg-1_all 
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.
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 JALVIEW(1)