jalview - Multiple alignment editor
jalview -open [FILE] [OUTPUT_FORMAT]
[OUTPUT_FILE]
Jalview provides facilities for viewing/editing and
otherwise manipulating sequence alignments (DNA, amino acids).
- -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.
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.