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)