Jalview Command Line Arguments (version 2.11.3.0 and later)

For a summary of Jalview command line arguments see Summary of Command Line Arguments.

From version 2.11.3.0 Jalview processes a new set of command line arguments which allow more powerful and flexible combinations of arguments, though can also be used for very simple use cases too.

These new arguments are all accessed with a --doubledash form of command line argument (with the one exception where simply opening one or more files can be performed without any arguments other than the filenames).

The old command line arguments can still be used (see the old page on command line arguments) so existing scripts utilising them should not break.

However, you cannot mix old and new style arguments, so if you use any -singledash arguments, they will all be interpreted as old style arguments with the new --doubledash arguments being ignored. If you have a script that uses the old arguments without any dashes, and uses the bare-word open then these will also be interpreted as old style arguments.
Note! If you use command line arguments without any dashes and don't use the bare-word argument open then all your arguments will be interpreted as alignment files to be opened by the new command line argument process.

Not everything that can be done with the old arguments is currently implemented in the new arguments but functionality of the new command line arguments will increase over releases. Significant new functionality, particularly allowing batch processing of files, is available in the new arguments.

To launch Jalview from the command line, see running Jalview from the command line.

Processing command line arguments

Jalview no longer necessarily processes arguments sequentially, although in typical use cases you may still want to think of it as doing so.
For more advanced use please see

Typical Use Cases

Opening files (--open, --append, --new)

To simply open one or more alignment files in different windows just put the filenames as the first arguments: 

  jalview filename1 filename2 ...

You can use shell-expanded wildcards: 

  jalview this/filename* that/filename* other/filename*
and URLs: 
  jalview https://rest.uniprot.org/uniprotkb/P00221.fasta

(Using initial filenames is the same as using the --open argument, and further arguments can be used after the initial filenames.)

--open

Use the --open argument to open alignment files each in their own window.

The following are equivalent: 

  jalview --open filename1 filename2 ...

  jalview --open filename*

  jalview --open filename1 --open filename2 --open ...

  jalview filename1 filename2 ...

Similarly you can open URLs: 

  jalview --open https://rest.uniprot.org/uniprotkb/P00221.fasta

--append

To append several alignment files together use: 

  jalview --open filename1.fa --append filename2.fa filename3.fa
or, if you haven't previously used --open then you can use --append to open one new window and keep appending each set of alignments: 
  jalview --append these/filename*.fa --append more/filename*.fa

  jalview --append https://rest.uniprot.org/uniprotkb/P00221.fasta https://www.uniprot.org/uniprotkb/A0A0K9QVB3/entry

Note that whilst you can include a Jalview Project File (.jvp) as an --append value, the items in the file will always open in their original windows and not append to another.

--new

To append different sets of alignment files in different windows, use --new to move on to a new alignment window: 

  jalview --append these/filename*.fa --new --append other/filename*.fa

--open is like using --new --append applied to every filename/URL given to --open

Alignment options (--colour, --wrap)

--colour

You can specify a residue/base colouring for the alignment using the --colour option (note spelling -- Jalview is made in Scotland!): 

  jalview --open examples/uniref50.fa --colour gecos-flower
There are several colour schemes that you can use. See the page on Colour Schemes for details. The names to use on the command line for colour schemes 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

--wrap

An alignment should open with your usual preferences stored in the .jalview_properties file. To open an alignment with the sequences (definitely) wrapped, following your --open (or first --append) argument use the argument --wrap: 

  jalview --open examples/uniref50.fa --wrap
To ensure an alignment is not wrapped use --nowrap: 
  jalview --open examples/uniref50.fa --nowrap

--annotations

You can specify whether the currently opened alignment window should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either --annotations or --noannotations. If you don't specify then your saved preference will be used. 

  jalview --open examples/uniref50.fa --noannotations

--title

If you would like to give the alignment window a specific title you can do so with the --title option: 

  jalview --open examples/uniref50.fa --title "My example alignment"

--structure

You can add a 3D structure file to a sequence in the current alignment window with the --structure option: 

  jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb

seqid: By default this attaches to the first sequence in the alignment but most likely you will want to attach it to another sequence. To do this you can specify a sub-value with the sequence ID, by preceding the value with square brackets and seqid=SequenceId like this: 

  jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
Remember that you might need to escape any spaces in the sequence ID or enclose the ID in quotation marks.

index: You can alternatively specify the (zero-indexed) index of the sequence within the alignment, although this is less precise. So to attach the structure to the 8th sequence use: 

  jalview --open examples/uniref50.fa --structure [7]examples/AlphaFold/AF-P00221-F1-model_v4.pdb

structureviewer: You can specify which structure viewer (or not) to use to open the structure using the structureviewer sub-value. Multiple sub-values can be specified, separated by a comma ','. Possible values for the structureviewer sub-value are:
none,
jmol,
chimera,
chimerax,
pymol.

none and jmol will always be available, but to use the others you must have the appropriate software already set up on your computer and in Jalview. See the page Discovering and Viewing PDB and 3D-Beacons structures for more details. 

  jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,structureviewer=none]examples/AlphaFold/AF-P00221-F1-model_v4.pdb

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