Jalview Command Line Arguments

Initialising arguments

-nodisplay

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

-props FILE/URL

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

-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. -

-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

Standalone executable jar only. - 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

Standalone executable jar only. - 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 physcial 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

+ 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

+ 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

✓

‑‑close

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

✓

Outputting alignment 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. +

✓

‑‑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.

✓

Exporting image files

argument

action

sub-value modifiers (optional)

linked (optional)

‑‑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.

✓

Exporting 3D structure image files (jmol only)

argument

action

sub-value modifiers (optional)

linked (optional)

‑‑structureimage filename

Export an image of a 3D structure opened in JMOL. Image formats can be: +
+ svg, +
+ png, +
+ eps. +

structureimagetype=name,
+      structureimagetextrenderer=name,
+      structureimagescale=number,
+      structureimagewidth=number,
+      structureimageheight=number
+

✓

‑‑structureimagetype name

Set the structure image format for the preceding --structureimage. Valid values are: +
+ svg, +
+ png, +
+ eps. +

✓

‑‑structureimagetextrenderer name

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

✓

‑‑structureimagescale number

Sets a scaling for bitmap structure image format (PNG). Should be given as a floating point number. If used in conjunction with --structureimagewidth and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image). +

✓

‑‑structureimagewidth number

Sets a width for bitmap structure image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image). +

✓

‑‑structureimageheight number

Sets a height for bitmap structure image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimagewidth then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image). +

✓

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 / ‑‑noall

Apply (or stop applying) the following output arguments to all sets of linked arguments.

‑‑allstructures / ‑‑noallstructures

+ Apply (or stop applying) the following 3D structure formatting arguments to all structures within the current open alignment. Whilst --allstructures will continue to operate for a --new alignment, the structure formatting arguments must be set again for each new alignment. +

‑‑quit

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

Command Line: summary

Initialising arguments

Opening an alignment

Adding a 3D structure

Processing alignments

Outputting alignment files

Exporting image files

Exporting 3D structure image files (`jmol` only)

Controlling flow of arguments

Command Line: summary

Initialising arguments

Opening an alignment

Adding a 3D structure

Processing alignments

Outputting alignment files

Exporting image files

Exporting 3D structure image files (jmol only)

Controlling flow of arguments

Exporting 3D structure image files (`jmol` only)