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 <[email protected]> and Pierre Gruet <[email protected]> from the Debian project, but may be used by others.