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+<title>Jalview Command Line Arguments: basic usage</title>
+<body>
+
+ <h1>Jalview Command Line Arguments: basic usage</h1>
+
+ <p>
+ <a href="clarguments.html">Jalview Command Line Arguments: summary</a>
+ <br/>
+ <a href="clarguments-intro.html">Jalview Command Line Arguments: introduction</a>
+ <br/>
+ Jalview Command Line Arguments: basic usage
+ <br/>
+ <a href="clarguments-advanced.html">Jalview Command Line Arguments: advanced usage</a>
+ <br/>
+ <a href="clarguments-argfiles.html">Jalview Command Line Arguments: argfiles</a>
+ </p>
+
+ <hr/>
+
+ <ul>
+ <li><a href="#openingalignments">Opening alignments</a></li>
+ <li><a href="#alignmentoptions">Alignment options</a></li>
+ <li><a href="#adding3dstructures">Adding 3D structures</a></li>
+ <li><a href="#outputtingalignmentfiles">Outputting/converting alignment files and images</a></li>
+ <li><a href="#filenamesubstitutionsandbatchprocessing">Filename substitutions and batch processing</a></li>
+ </ul>
+
+ <h2><a name="openingalignments"></a>Opening alignments (<code>--open</code>, <code>--append</code>, <code>--new</code>)</h2>
+
+ <p>
+ To simply open one or more alignment files in different windows just put the filenames as the first arguments:
+ <pre>
+ jalview filename1 filename2 ...
+ </pre>
+ </p>
+
+ <p>
+ You can use shell-expanded wildcards:
+ <pre>
+ jalview this/filename* that/filename* other/filename*
+ </pre>
+ and URLs:
+ <pre>
+ jalview https://rest.uniprot.org/uniprotkb/P00221.fasta
+ </pre>
+ </p>
+
+ <p>
+ (Using initial filenames is the same as using the <code>--open</code> argument, and further arguments can be used
+ after the initial filenames.)
+ </p>
+
+ <h3><a name="open"></a><code>--open</code></h3>
+
+ <p>
+ Use the <code>--open</code> argument to open alignment files each in their own window.
+ </p>
+
+ <p>
+ The following are equivalent:
+ <pre>
+ jalview --open filename1 filename2 ...
+
+ jalview --open filename*
+
+ jalview --open filename1 --open filename2 --open ...
+
+ jalview filename1 filename2 ...
+ </pre>
+ </p>
+
+ <p>
+ Similarly you can open URLs:
+ <pre>
+ jalview --open https://rest.uniprot.org/uniprotkb/P00221.fasta
+ </pre>
+ </p>
+
+ <h3><a name="append"></a><code>--append</code></h3>
+
+ <p>
+ To append several alignment files together use:
+ <pre>
+ jalview --open filename1.fa --append filename2.fa filename3.fa
+ </pre>
+ or, if you haven't previously used <code>--open</code> then you can use --append to open one new window and keep appending each set of alignments:
+ <pre>
+ 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
+ </pre>
+ </p>
+
+ <p>
+ <strong>Note</strong> that whilst you can include a Jalview Project File (<code>.jvp</code>) as an <code>--append</code> value, the items in the file will always open in their original windows and not append to another.
+ </p>
+
+ <h3><a name="new"></a><code>--new</code></h3>
+
+ <p>
+ To append different sets of alignment files in different windows, use <code>--new</code> to move on to a new alignment window:
+ <pre>
+ jalview --append these/filename*.fa --new --append other/filename*.fa
+ </pre>
+ </p>
+
+ <p>
+ <code>--open</code> is like using <code>--new --append</code> applied to every filename/URL given to <code>--open</code>
+ </p>
+
+
+ <h2><a name="alignmentoptions"></a>Alignment options (<code>--colour</code>, <code>--wrap</code>, <code>--showannotations</code>, <code>--title</code>)</h2>
+
+ <h3><a name="colour"></a><code>--colour</code></h3>
+
+ <p>
+ You can specify a residue/base colouring for the alignment using the <code>--colour</code> option (note spelling -- Jalview is made in Scotland!):
+ <pre>
+ jalview --open examples/uniref50.fa --colour gecos-flower
+ </pre>
+ There are several colour schemes that you can use. See the <a href="../colourSchemes/index.html">page on Colour Schemes</a> for details.
+ The names to use on the command line for colour schemes are:
+ </p>
+ <p>
+ <code>clustal</code>,
+ <br/>
+ <code>blosum62</code>,
+ <br/>
+ <code>pc-identity</code>,
+ <br/>
+ <code>zappo</code>,
+ <br/>
+ <code>taylor</code>,
+ <br/>
+ <code>gecos-flower</code>,
+ <br/>
+ <code>gecos-blossom</code>,
+ <br/>
+ <code>gecos-sunset</code>,
+ <br/>
+ <code>gecos-ocean</code>,
+ <br/>
+ <code>hydrophobic</code>,
+ <br/>
+ <code>helix-propensity</code>,
+ <br/>
+ <code>strand-propensity</code>,
+ <br/>
+ <code>turn-propensity</code>,
+ <br/>
+ <code>buried-index</code>,
+ <br/>
+ <code>nucleotide</code>,
+ <br/>
+ <code>nucleotide-ambiguity</code>,
+ <br/>
+ <code>purine-pyrimidine</code>,
+ <br/>
+ <code>rna-helices</code>,
+ <br/>
+ <code>t-coffee-scores</code>,
+ <br/>
+ <code>sequence-id</code>
+ </p>
+
+ <h3><a name="wrap"></a><code>--wrap</code></h3>
+ <p>
+ An alignment should open with your usual preferences stored in the <code>.jalview_properties</code> file. To open an alignment with the sequences (definitely) wrapped, following your <code>--open</code> (or first <code>--append</code>) argument use the argument <code>--wrap</code>:
+ <pre>
+ jalview --open examples/uniref50.fa --wrap
+ </pre>
+ To ensure an alignment is not wrapped use <code>--nowrap</code>:
+ <pre>
+ jalview --open examples/uniref50.fa --nowrap
+ </pre>
+ </p>
+
+ <h3><a name="showannotations"></a><code>--showannotations</code> / <code>--noshowannotations</code></h3>
+
+ <p>
+ You can specify whether the currently opened alignment window should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either <code>--showannotations</code> or <code>--noshowannotations</code>. If you don't specify then your saved preference will be used.
+ <pre>
+ jalview --open examples/uniref50.fa --noshowannotations
+ </pre>
+ </p>
+
+ <h3><a name="title"></a><code>--title</code></h3>
+
+ <p>
+ If you would like to give the alignment window a specific title you can do so with the <code>--title</code> option:
+ <pre>
+ jalview --open examples/uniref50.fa --title "My example alignment"
+ </pre>
+ </p>
+
+
+
+
+ <h2><a name="adding3dstructures"></a>Adding 3D structures (<code>--structure</code>, <code>--seqid</code>, <code>--structureviewer</code>, <code>--paematrix</code>, <code>--tempfac</code>, <code>--showssannotations</code>)</h2>
+
+ <p>
+ </p>
+
+ <h3><a name="structure"></a><code>--structure</code></h3>
+
+ <p>
+ You can add a 3D structure file to a sequence in the current alignment window with the <code>--structure</code> option:
+ <pre>
+ jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+ By default this attaches to the first sequence in the alignment but most likely you will want to attach it to a specific sequence.
+ </p>
+
+ <h3><a name="seqid"></a><code>--seqid</code></h3>
+
+ <p>
+ The easiest way to specify a sequence ID for your structure is to follow the <code>--structure</code> argument with a <code>--seqid</code> argument with a value of a sequence ID in the alignment. This does of course require some knowledge of the sequences in the alignment files
+ that have been opened.
+ <br/>
+ Alternatively you can specify a <em>sub-value</em> with the <code>--structure</code> argument value. You do this by preceding the value with square brackets and <code>seqid=SequenceId</code>,
+ like this:
+ <pre>
+ jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+ which is equivalent to
+ <pre>
+ jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --seqid FER1_SPIOL
+ </pre>
+ </p>
+
+ <p>
+ The sub-value <code>seqid=FER1_SPIOL</code> takes precedence over the following argument <code>--seqid FER1_SPIOL</code> if you accidentally specify both (in which case the argument will probably be completely unused).
+ </p>
+
+ <p>
+ If you don't know the sequence IDs but do know the position of the sequence in the alignment, you can also specify an <em>INDEX</em>
+ in the sub-values to indicate which sequence in the alignment to attach the sequence to (although this is less precise). This is a zero-indexed value, so to specify the eighth sequence in the alignment use:
+ <pre>
+ jalview --open examples/uniref50.fa --structure [7]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+
+ <p>
+ Remember that you might need to escape any spaces in the sequence ID or enclose the ID in quotation marks.
+ </p>
+
+ <h3><a name="structureviewer"></a><code>--structureviewer</code></h3>
+
+ <p>
+ You can specify which structure viewer (or none) to use to open the structure using either the <code>--structureviewer</code> argument or the <code>structureviewer</code> sub-value. Multiple sub-values can be specified together, separated by a comma ','. Possible values for the <code>structureviewer</code> are:
+ <br/>
+ <code>none</code>,
+ <br/>
+ <code>jmol</code>,
+ <br/>
+ <code>chimera</code>,
+ <br/>
+ <code>chimerax</code>,
+ <br/>
+ <code>pymol</code>.
+ </p>
+ <p>
+ <code>none</code> and <code>jmol</code> 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 <a href="../features/viewingpdbs.html">Discovering and Viewing PDB and 3D-Beacons structures</a> for more details.
+ <pre>
+ jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,structureviewer=none]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+ or, if you prefer
+ <pre>
+ jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --seqid FER1_SPIOL --structureviewer none
+ </pre>
+ </p>
+
+ <h3><a name="paematrix"></a><code>--paematrix</code></h3>
+
+ <p>
+ If you are opening a structure file that has a PAE matrix (provided as a JSON file), such as from an AlphaFold model or an nf-core pipeline, you can add the PAE matrix as an annotation by following the <code>--structure</code> argument with a <code>--paematrix</code> argument with the filename. You can also specify a <code>paematrix=filename</code> sub-value.
+ <pre>
+ jalview --open examples/uniref50.fa --structure [seqid=FER1+SPIOL,structureviewer=pymol]examples/AlphaFold/AF-P00221-F1-model_v4.pdb --paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json
+ </pre>
+ </p>
+
+ <h3><a name="tempfac"></a><code>--tempfac</code></h3>
+
+ <p>
+ Structure files may have a temperature factor associated with the structure component positions. If the temperature factor is a pLDDT confidence score, such as with an AlphaFold model, you can specify this by using a following argument of <code>--tempfac</code> with a value of <code>plddt</code>. This will enable standard pLDDT colouring of the temperature factor annotation. Valid values are:
+ <code>default</code>,
+ <code>plddt</code>.
+ More types of temperature factor may be added in future releases of Jalview.
+ <br/>
+ The value can also be specified as a sub-value:
+ <pre>
+ jalview --open examples/uniref50.fa --structure [seqid=FER1+SPIOL,structureviewer=jmol,tempfac=plddt]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+ which is equivalent to
+ <pre>
+ jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --tempfac plddt --seqid FER1+SPIOL
+ --structureviewer jmol
+ </pre>
+
+ </p>
+
+ <!-- notempfac not yet working. undocumented until then -->
+
+ <h3><a name="showssannotations"></a><code>--showssannotations</code> / <code>--noshowssannotations</code></h3>
+
+ <p>
+ You can specify whether the currently opened alignment window should show secondary structure annotations or not with either <code>--showssannotations</code> or <code>--noshowssannotations</code>. If you don't specify then your saved preference will be used.
+ <pre>
+ jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --noshowssannotations
+ </pre>
+ or you can use a sub-value modifier:
+ <pre>
+ jalview --open examples/uniref50.fa --structure [noshowssannotations]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+ </pre>
+ </p>
+
+ <h2><a name="outputtingalignmentfiles"></a>Outputting/converting alignment files and images (<code>--output</code>, <code>--format</code>, <code>--image</code>, <code>--type</code>, <code>--textrenderer</code>, <code>--scale</code>, <code>--backups</code>, <code>--overwrite</code>)</h2>
+
+ <p>
+ You can save an alignment as an alignment file, or exported as an image, in different formats. Jalview's alignment output formats are:
+ fasta,
+ pfam,
+ stockholm,
+ pir,
+ blc,
+ amsa,
+ json,
+ pileup,
+ msf,
+ clustal,
+ phylip,
+ jalview.
+ </p>
+ <p>
+ Alignments can be exported as an image in formats EPS, SVG, HTML, BioJSON (vector formats) or PNG (bitmap format).
+ </p>
+ <p>
+ In vector formats you can specify whether text should be rendered as text (which may have font changes, but will produce a smaller and more usable file) or as lineart (which will retain exact appearance of text, but will be less easy to edit or use to copy text).
+ </p>
+ <p>
+ In bitmap formats (currently only PNG, but what else would you want?!) you can specify a scaling factor to improve the resolution of the output image.
+ </p>
+
+ <h3><a name="output"></a><code>--output</code></h3>
+
+ <p>
+ To save the open alignment in a new alignment file use <code>--output filename</code>. The format for the file can be found from the extension of <code>filename</code>, or if you are using a non-standard extension you can use a following <code>--format</code> argument, or specify it as a sub-value modifier.
+ </p>
+ <p>
+ Recognised formats and their recognised extensions are:
+ <br/>
+ <code>fasta</code> (<code>fa, fasta, mfa, fastq</code>),
+ <br/>
+ <code>pfam</code> (<code>pfam</code>),
+ <br/>
+ <code>stockholm</code> (<code>sto, stk</code>),
+ <br/>
+ <code>pir</code> (<code>pir</code>),
+ <br/>
+ <code>blc</code> (<code>blc</code>),
+ <br/>
+ <code>amsa</code> (<code>amsa</code>),
+ <br/>
+ <code>json</code> (<code>json</code>),
+ <br/>
+ <code>pileup</code> (<code>pileup</code>),
+ <br/>
+ <code>msf</code> (<code>msf</code>),
+ <br/>
+ <code>clustal</code> (<code>aln</code>),
+ <br/>
+ <code>phylip</code> (<code>phy</code>),
+ <br/>
+ <code>jalview</code> (<code>jvp, jar</code>).
+ <p>
+ For example, to open a FASTA file, append another FASTA file and then save the concatenation as a Stockholm file, do
+ <pre>
+ jalview --open alignment1.fa --append alignment2.fa --output bothalignments.stk
+ </pre>
+ or
+ <pre>
+ jalview --append alignment*.fa --output bigballofstring.txt --format stockholm
+ </pre>
+ or
+ <pre>
+ jalview --append alignment*.fa --output [format=stockholm]bigballofstring.txt
+ </pre>
+ </p>
+
+ <h3><a name="format"></a><code>--format</code></h3>
+
+ <p>
+ To specify the format of the output file (if using an unrecognised file extension) use the <code>--format</code> argument to specify a value (see above). A sub-value modifier on the <code>--output</code> value can also be used.
+ </p>
+
+ <h3><a name="image"></a><code>--image</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+
+ <h2><a name="filenamesubstitutionsandbatchprocessing"></a>Filename substitutions and batch processing (<code>--substitutions</code>, <code>--new</code>, <code>--close</code>, <code>--all</code>)</h2>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ <h3><a name=""></a><code>--</code></h3>
+
+ <p>
+ <pre>
+ </pre>
+ </p>
+
+ Continue to <a href="clarguments-advanced.html">Jalview Command Line Arguments: advanced usage</a>.
+
+
+
+</body>
+</html>
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