See Jalview Command Line Arguments (next generation) for more explanation about using Jalview's command line arguments.
| argument | action | subval modifiers (optional) | linked (optional) |
--open filename/URL ... |
Opens one or more alignment files filename or URLs URL in new alignment windows. Examples. |
colour=colourscheme,
title=title,
features=featurefile,
annotations=annotationfile,
tree=treefile,
showannotations,
ssannotations,
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=title,
features=featurefile,
annotations=annotationfile,
tree=treefile,
showannotations,
ssannotations,
sortbytree,
wrap
.
Examples.
|
✓ |
--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 nameare:
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.
Examples.
| ✓ | |
--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. | ✓ | |
--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 subval modifier seqid=ID can be used. A subval INDEX can also be used to specify the INDEX-th sequence in the open alignment. |
seqid=sequenceid or INDEX,
paefile=paefilename,
tempfac=temperature factor type,
ssannotations,
notempfac,
structureviewer=structure viewer
|
✓ |
--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. Possible 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. Possible 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
|
✓ | |
--notempfac |
Do not show the temperature factor annotation for the preceding --structure |
✓ | |
--groovy filename |
Process a groovy script in the file for the open alignment. | ✓ | |
--image new filename |
Output an image of the open alignment window. Format is specified by the subval modifier, a following --type argument or guessed from the file extension. Valid formats/extensions are:
svg,
png,
eps,
html,
biojs
|
type=image format,
|
✓ |
--type image format |
Set the image format for the preceding --image. Valid values are:
svg,
png,
eps,
html,
biojs
|
✓ | |
--textrenderer text format |
Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values are:
text,
lineart
|
✓ | |
--output outputfilename |
Export the open alignment. Format is specified by the subval modifier, a following --format argument or guessed from the file extension. Valid formats/extensions are:
Fasta ( fa, fasta),
|
✓ | |
-- |
✓ | ||
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✓ | ||
-- |
✓ |