.\"                                      Hey, EMACS: -*- nroff -*-
.\" First parameter, NAME, should be all caps
.\" Copyright 2011 by Vincent Fourmond
.\" Can be modified and distributed under the terms of the GNU General
.\" public license, version 3 or any later version at your option.
.TH JALVIEW  1  "06-02-2021"
.SH NAME
jalview \- Multiple alignment editor
.SH SYNOPSIS
.B \fBjalview\fP \-open [\fIFILE\fP] [\fIOUTPUT_FORMAT\fP] [\fIOUTPUT_FILE\fP]

.SH DESCRIPTION

.B Jalview
provides facilities for viewing/editing and otherwise manipulating
sequence alignments (DNA, amino acids).

.SH OPTIONS
.TP
.BR \-nodisplay
Run
.B Jalview 
without User Interface.
.TP
.BR \-props " FILE"
Use the given
.B Jalview  
properties file instead of users default.
.TP
.BR \-colour " COLOURSCHEME"
The colourscheme to be applied to the alignment
.TP
.BR \-annotations " FILE"
Add precalculated annotations to the alignment.
.TP
.BR \-tree " FILE"
Load the given newick format tree file onto the alignment
.TP
.BR \-features " FILE"
Use the given file to mark features on the alignment.
.TP
.BR \-fasta " FILE"
Create alignment file FILE in Fasta format.
.TP
.BR \-clustal " FILE"
Create alignment file FILE in Clustal format.
.TP
.BR \-pfam " FILE"
Create alignment file FILE in PFAM format.
.TP
.BR \-msf " FILE"
Create alignment file FILE in MSF format.
.TP
.BR \-pileup " FILE"
Create alignment file FILE in Pileup format
.TP
.BR \-pir " FILE"
Create alignment file FILE in PIR format.
.TP
.BR \-blc " FILE"
Create alignment file FILE in BLC format.
.TP
.BR \-json " FILE"
Create alignment file FILE in JSON format.
.TP
.BR \-jalview " FILE"
Create alignment file FILE in
.B Jalview 
format.
.TP
.BR \-png " FILE"
Create PNG image FILE from alignment.
.TP
.BR \-svg " FILE"
Create SVG image FILE from alignment.
.TP
.BR \-html " FILE"
Create HTML file from alignment.
.TP
.BR \-biojsMSA " FILE"
Create BioJS MSA Viewer HTML file from alignment.
.TP
.BR \-imgMap " FILE"
Create HTML file FILE with image map of PNG image.
.TP
.BR \-eps " FILE"
Create EPS file FILE from alignment.
.TP
.BR \-questionnaire " URL"
Queries the given URL for information about any
.B Jalview 
user questionnaires.
.TP
.BR \-noquestionnaire
Turn off questionnaire check.
.TP
.BR \-nonews
Turn off check for Jalview news.
.TP
.BR \-nohtmltemplates
Disable the automatic download of templates in the Github repository.
.TP
.BR \-sortbytree " OR " \-nosortbytree
Enable or disable sorting of the given alignment by the given tree
.TP
.BR \-jabaws " URL"
Specify URL for Jabaws services (e.g. for a local installation).
.TP
.BR \-fetchfrom " nickname"
Query nickname for features for the alignments and display them.
.TP
.BR \-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).
.TP
.BR \-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.
.TP
.BR \-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.
.TP

.SH SEE ALSO

.B https://www.jalview.org

.SH 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.