.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
.TH VARNA "1" "August 2022" "varna 3-93+ds" "User Commands"
.SH NAME
varna \- Assisted drawing of RNA secondary structure
.SH SYNOPSIS
.B java
\fI\,-cp . \/\fR[\fI\,-i InFile|-sequenceDBN XXX -structureDBN YYY\/\fR] \fI\,-o OutFile \/\fR[\fI\,Options\/\fR]
.SH DESCRIPTION
VARNA v3.9 Assisted drawing of RNA secondary structure (Command Line version)
.SS "Where:"
.TP
OutFile
Supported formats: {JPEG,PNG,EPS,XFIG,SVG}
.TP
InFile
Secondary structure file: Supported formats: {BPSEQ,CT,RNAML,DBN}
.SS "Main options:"
.TP
\fB\-algorithm\fR
Drawing algorithm, choosen from [naview,line,radiate,circular]
.TP
\fB\-backbone\fR
Backbone color (Ex: #334455)
.TP
\fB\-baseInner\fR
Default value for inner base color (Ex: #334455)
.TP
\fB\-baseOutline\fR
Base outline color (Ex: #334455)
.TP
\fB\-bp\fR
Base pair color (Ex: #334455)
.TP
\fB\-bpStyle\fR
Look and feel for base pairs drawings, choosen from [lw,lwalt,none,simple,rnaviz]
.TP
\fB\-h\fR
Displays a short description of main options and exits
.TP
\fB\-periodNum\fR
Periodicity of base\-numbering
.TP
\fB\-x\fR
Displays a detailled description of all options
.SS "Advanced options:"
.TP
\fB\-annotations\fR
A set of textual annotations
.TP
\fB\-applyBasesStyle\fR
Base style application
.HP
\fB\-autoHelices\fR
.HP
\fB\-autoInteriorLoops\fR
.HP
\fB\-autoTerminalLoops\fR
.TP
\fB\-auxBPs\fR
Adds a list of (possibly non\-canonical) base\-pairs to those already defined by
the main secondary structure (Ex: "(1,10);(2,11);(3,12)"). Custom BP styles c
.IP
an be specified (Ex: "(2,11):thickness=4;(3,12):color=#FF0000").
.TP
\fB\-background\fR
Background color (Ex: #334455)
.TP
\fB\-baseName\fR
Residues font color (Ex: #334455)
.TP
\fB\-baseNum\fR
Base numbers font color (Ex: #334455)
.TP
\fB\-basesStyle\fR
Base style declaration
.TP
\fB\-border\fR
Border width and height in pixels (Ex: "20x40")
.TP
\fB\-bpIncrement\fR
Distance between nested base\-pairs (i.e. arcs) in linear representation
.HP
\fB\-chemProb\fR
.TP
\fB\-colorMap\fR
Associates a list of numerical values (eg '0.2,0.4,0.6,0.8') with the RNA base
s with respect to their natural order, and modifies the color used to fill the
se bases according to current color map style.
.TP
\fB\-colorMapCaption\fR
Sets current color map caption.
.HP
\fB\-colorMapMax\fR
.HP
\fB\-colorMapMin\fR
.TP
\fB\-colorMapStyle\fR
Selects a specific color map style. It can be either one of the predefined sty
les (eg 'red', 'green', 'blue', 'bw', 'heat', 'energy') or a new one (eg '0:#F
FFF00;1:#ffFFFF;6:#FF0000').
.TP
\fB\-columns\fR
Sets number of rows
.TP
\fB\-comparisonMode\fR
Activates comparison mode
.HP
\fB\-customBPs\fR
.HP
\fB\-customBases\fR
.TP
\fB\-drawBackbone\fR
True if the backbone must be drawn, false otherwise
.TP
\fB\-drawBases\fR
Shows/hide the outline of bases
.HP
\fB\-drawColorMap\fR
.TP
\fB\-drawNC\fR
Toggles on/off display of non\-canonical base\-pairs
.TP
\fB\-drawTertiary\fR
Toggles on/off display of tertiary interaction, ie pseudoknots
.TP
\fB\-error\fR
Show errors
.TP
\fB\-fillBases\fR
Fills or leaves empty the inner portions of bases
.TP
\fB\-firstSequence\fR
In comparison mode, sequence of first RNA
.TP
\fB\-firstStructure\fR
In comparison mode, structure of first RNA
.TP
\fB\-flat\fR
Toggles on/off (true/false) drawing exterior bases on a straight line
.TP
\fB\-flip\fR
Draws a set of exterior helices, identified by the argument string, in clockwi
se order (default drawing is counter\-clockwise). The argument is a semicolon\-s
eparated list of helices, each identified by a base or a base\-pair (eg. "2;20\-
34").
.TP
\fB\-gapsColor\fR
Define and use custom color for gaps bases in comparison mode
.TP
\fB\-highlightRegion\fR
Highlight a set of contiguous regions
.TP
\fB\-modifiable\fR
Allows/prohibits modifications
.TP
\fB\-nsBasesColor\fR
Define and use custom color for non\-standard bases in comparison mode
.TP
\fB\-orientation\fR
Sets the general orientation of an RNA, i.e. the deviation of the longest axis
(defined by the most distant couple of bases) from the horizontal axis.
.TP
\fB\-quality\fR
Sets quality (non\-vector file formats only)
.TP
\fB\-resolution\fR
Sets resolution (non\-vector file formats only)
.TP
\fB\-rotation\fR
Rotates RNA after initial drawing (Ex: '20' for a 20 degree counter\-clockwise
rotation)
.TP
\fB\-rows\fR
Sets number of columns
.TP
\fB\-secondSequence\fR
In comparison mode, sequence of second RNA
.TP
\fB\-secondStructure\fR
In comparison mode, structure of second RNA
.TP
\fB\-sequenceDBN\fR
Raw RNA sequence
.TP
\fB\-spaceBetweenBases\fR
Sets the space between consecutive bases
.TP
\fB\-structureDBN\fR
RNA structure given in dot bracket notation (DBN)
.TP
\fB\-title\fR
RNA drawing title
.TP
\fB\-titleColor\fR
Title color (Ex: #334455)
.TP
\fB\-titleSize\fR
Title font size
.TP
\fB\-warning\fR
Show warnings
.TP
\fB\-zoom\fR
Zoom coefficient
.TP
\fB\-zoomAmount\fR
Zoom increment on user interaction