Jalview Command Line Arguments

Jalview Command Line Arguments: summary

running Jalview from the command line

'JVL' file

memory settings

- jalview -open <Alignment File/URL> [additional import arguments] [export arguments] -

Initialising arguments

-nodisplay

Run Jalview without - User Interface. (automatically disables questionnaire, version - and usage stats checks)

-nowebservicediscovery

Do not query configured servers to - discover web services (Since 2.11.2.0)

-open FILE/URL

Specify the alignment file to - open or process by providing additional arguments.

-props FILE/URL

Use the given Jalview properties - file instead of users default.

-setprop PROPERTY=value

(JalviewJS ONLY) sets the given - property to the given value

-features FILE/URL

- Use the given file to add sequence features to an alignment. - See Features - File (Known as Groups file prior to 2.08) description. -

- -

-colour COLOURSCHEME

Set the colourscheme for the alignment. This can be any - of the built-in colourschemes, a name of a predefined - colourscheme (defined in the Jalview properties file), or an - 'inline' colourscheme (see the applet's colour parameter for - more information).

-annotations FILE/URL

Add precalculated annotations to the alignment. See Annotation - File description. -

-no-annotation

Do not display annotation below the alignment. -

-tree FILE/URL

Load the given newick format tree file - onto the alignment

-questionnaire URL

Queries the given URL for information - about any Jalview user questionnaires

-noquestionnaire

Turn off questionnaire check

-nonews

- Disable check for Jalview - news on startup (not recommended other than for classroom / - demo usage) -

-nousagestats

Turn off google analytics usage tracking

-[no]sortbytree

Enable or disable automatic sorting of - associated view when a new tree is displayed

-groovy FILE/URL

Execute groovy script in FILE (where - FILE may be 'STDIN' to read from the standard input) after all - other arguments have been processed

-jabaws URL

Specify the URL of the preferred JABAWS - server

-fasta FILE

Create alignment file FILE in Fasta - format.

-clustal FILE

Create alignment file FILE in - Clustal 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.

-pfam FILE

Create alignment file FILE in - PFAM 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.

-imgMap FILE

Create HTML file FILE with image - map of PNG image.

-eps FILE

Create EPS file FILE from - alignment.

-svg FILE

Create Scalable Vector Graphics - file FILE from alignment.

-biojsMSA FILE

Write an HTML page to display - the alignment with the - BioJS MSAviewer MSA -

-jvmmempc=PERCENT

Only available with standalone executable jar or jalview.bin.Launcher. - Limit maximum heap size (memory) to PERCENT% of total physical memory detected. - This defaults to 90 if total physical memory can be detected. - See Memory usage settings for Jalview 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 Memory usage settings for Jalview for more details. -

argument

action

‑‑help / -h

Display a help statement

‑‑headless

Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.

‑‑jabaws URL

Set a different URL to connect to a JABAWS server.

‑‑news / ‑‑nonews

Show (or don't show) the news feed.

‑‑splash / ‑‑nosplash

Show (or don't show) the About Jalview splash screen.

‑‑questionnaire / ‑‑noquestionnaire

Show (or don't show) the questionnaire if one is available.

‑‑usagestats / ‑‑nousagestats

Send (or don't send) initial launch usage stats. Note: usage stats are useful for future funding for Jalview!

‑‑webservicediscovery / ‑‑nowebservicediscovery

Attempt (or don't attempt) to connect to JABAWS web services.

‑‑props filename

Use file filename as the preferences file instead of the usual ~/.jalview_properties file.

‑‑debug

Start Jalview in debug log level.

‑‑quiet

Stop all output to STDOUT (after the Java Virtual Machine has started). Use ‑‑quiet a second time to stop all output to STDERR.

‑‑initsubstitutions / ‑‑noinitsubstitutions

Set ‑‑substitutions to be initially enabled (or initially disabled).

‑‑jvmmempc=PERCENT

+ Only available with standalone executable jar or jalview.bin.Launcher. +
+ Limit maximum heap size (memory) to PERCENT% of total physical memory detected. + This defaults to 90 if total physical memory can be detected. +
+ The equals sign ("=") separator must be used with no spaces. +
+ See Memory usage settings for Jalview 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. +
+ The equals sign ("=") separator must be used with no spaces. +
+ See Memory usage settings for Jalview for more details. +

Opening an alignment

argument

action

sub-value modifiers (optional)

linked (optional)

‑‑open filename/URL ...

+ Opens one or more alignment files filename or URLs URL in new alignment windows. +


+        colour=name,
+        

+        title=string,
+        

+        features=filename,
+        

+        annotations=filename,
+        

+        tree=filename,
+        

+        showannotations,
+        

+        showssannotations,
+        

+        sortbytree,
+        

+        wrap
+

✓

‑‑append filename/URL ...

Appends one or more alignment files filename or URLs URL to the open alignment window (or opens a new alignment if none already open).


+        colour=name,
+        

+        title=string,
+        

+        features=filename,
+        

+        annotations=filename,
+        

+        tree=filename,
+        

+        showannotations,
+        

+        showssannotations,
+        

+        sortbytree,
+        

+        wrap
+

✓

‑‑title "string""

Specifies the title for the open alignment window as string.

✓

‑‑colour name

Applies the colour scheme name to the open alignment window. Valid values for name are: +
+ clustal, +
+ blosum62, +
+ pc-identity, +
+ zappo, +
+ taylor, +
+ gecos-flower, +
+ gecos-blossom, +
+ gecos-sunset, +
+ gecos-ocean, +
+ hydrophobic, +
+ helix-propensity, +
+ strand-propensity, +
+ turn-propensity, +
+ buried-index, +
+ nucleotide, +
+ nucleotide-ambiguity, +
+ purine-pyrimidine, +
+ rna-helices, +
+ t-coffee-scores, +
+ sequence-id. +

✓

‑‑features filename/URL

Add a feature file filename or URL URL to the open alignment.

✓

‑‑tree filename/URL

Add a tree file filename or URL URL to the open alignment.

✓

‑‑sortbytree / ‑‑nosortbytree

Enforces sorting (or not sorting) the alignment in the order of an attached phylogenetic tree.

✓

‑‑annotations filename/URL

Add an annotations file filename or URL URL to the open alignment.

✓

‑‑showannotations / ‑‑noshowannotations

Enforces showing (or not showing) alignment annotations.

✓

‑‑wrap / ‑‑nowrap

Enforces wrapped (or not wrapped) alignment formatting.

✓

‑‑nostructure

Do not open or process any 3D structure in the ‑‑open or ‑‑append files.

✓

Adding a 3D structure

argument

action

sub-value modifiers (optional)

linked (optional)

‑‑structure filename/URL

Load a structure file filename or URL URL associated with a sequence in the open alignment. The sequence to be associated with can be specified with a following ‑‑seqid argument, or the sub-value modifier seqid=ID can be used. A sub-value INDEX can also be used to specify the INDEX-th sequence in the open alignment.


+        seqid=id

INDEX,
+        

+        paefile=filename,
+        

+        tempfac=name,
+        

+        showssannotations,
+        
+        

+        structureviewer=name
+

✓

‑‑seqid ID

Specify the sequence name for the preceding ‑‑structure to be associated with.

✓

‑‑paematrix filename

Add a PAE json matrix file filename to the preceding ‑‑structure.

✓

‑‑tempfac name

Set the type of temperature factor. Valid values for name are: +
+ default, +
+ plddt +

✓

‑‑structureviewer name

Set the structure viewer to use to open the 3d structure file specified in previous ‑‑structure to name. Valid values of name are: +
+ none, +
+ jmol, +
+ chimera - requires installation, might need configuring in Preferences, +
+ chimerax - requires installation, might need configuring in Preferences, +
+ pymol - requires installation, might need configuring in Preferences +

✓

‑‑showssannotations / ‑‑noshowssannotations

Do not show secondary structure annotations for the preceding ‑‑structure

✓

Outputting files

argument

action

sub-value modifiers (optional)

linked (optional)

‑‑output filename

Export the open alignment to file filename. The format name is specified by the sub-value modifier format=name, a following ‑‑format name argument or guessed from the file extension. Valid format names (and file extensions) are: +
+ fasta (fa, fasta, mfa, fastq), +
+ pfam (pfam), +
+ stockholm (sto, stk), +
+ pir (pir), +
+ blc (blc), +
+ amsa (amsa), +
+ json (json), +
+ pileup (pileup), +
+ msf (msf), +
+ clustal (aln), +
+ phylip (phy), +
+ jalview (jvp, jar). +

format=name

✓

‑‑format name

Sets the format for the preceding ‑‑output file. Valid formats are: +
+ fasta, +
+ pfam, +
+ stockholm, +
+ pir, +
+ blc, +
+ amsa, +
+ json, +
+ pileup, +
+ msf, +
+ clustal, +
+ phylip, +
+ jalview. +

✓

‑‑image filename

Output an image of the open alignment window. Format is specified by the sub-value modifier, a following ‑‑type argument or guessed from the file extension. Valid formats/extensions are: +
+ svg, +
+ png, +
+ eps, +
+ html, +
+ biojs. +

type=name,
+      textrenderer=name,
+      scale=number,
+      width=number,
+      height=number
+

✓

‑‑type name

Set the image format for the preceding ‑‑image to name. Valid values for name are: +
+ svg, +
+ png, +
+ eps, +
+ html, +
+ biojs. +

✓

‑‑textrenderer name

Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Valid values for name are: +
+ text, +
+ lineart. +

✓

‑‑scale number

Sets a scaling for bitmap image format (PNG). Should be given as a floating point number. This can also be set as a sub-value modifier to the --image value. If used in conjunction with --width and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).

✓

‑‑width number

Sets a width for bitmap image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. This can also be set as a sub-value modifier to the --image value. If used in conjunction with --scale and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).

✓

‑‑height number

Sets a height for bitmap image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. This can also be set as a sub-value modifier to the --image value. If used in conjunction with --scale and --width then the smallest scaling will be used (scale, width and height provide bounds for the image).

✓

‑‑groovy filename

Process a groovy script in the file for the open alignment.

✓

‑‑backups / ‑‑nobackups

Enable (or disable) writing backup files when saving an ‑‑output file. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.

✓

‑‑overwrite / ‑‑nooverwrite

Enable (or disable) overwriting of output files without backups enabled. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.

✓

‑‑close

Close the current open alignment window. This occurs after other output arguments. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.

✓

Controlling flow of arguments

argument

action

‑‑new

+ Move on to a new alignment window. This will ensure ‑‑append will start a new alignment window and other linked arguments will apply to the new alignment window. +
+ Note that --open already starts a new alignment window for each file it opens. +

‑‑substitutions / ‑‑nosubstitutions

The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are + {basename} - the filename-without-extension of the currently ‑‑opened file (or first ‑‑appended file), +
+ {dirname}, - the directory (folder) name of the currently ‑‑opened file (or first ‑‑appended file), +
+ {argfilebasename} - the filename-without-extension of the current ‑‑argfile, +
+ {argfiledirname} - the directory (folder) name of the current ‑‑argfile, +
+ {n} - the value of the index counter (starting at 0). +
+ {++n} - increase and substitute the value of the index counter, +
+ {} - the value of the current alignment window default index. +

‑‑argfile filename

+ Open one or more files filename and read, line-by-line, as arguments to Jalview. +
+ Values in an argfile should be given with an equals sign ("=") separator with no spaces. +
+ Note that if you use one or more ‑‑argfile arguments then all other non-initialising arguments will be ignored. +

‑‑npp

Increase the index counter used in argument value substitutions.

‑‑all

Apply the following output arguments to all sets of linked arguments.

‑‑quit

After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.