.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
.TH WEBLOGO "1" "November 2022" "WebLogo 3.7.12" "User Commands"
.SH NAME
WebLogo \- create sequence logos from biological sequence alignments
.SH SYNOPSIS
.B weblogo
[\fI\,options\/\fR]  \fI\,< sequence_data.fa > sequence_logo.eps\/\fR
.SH DESCRIPTION
Create sequence logos from biological sequence alignments.
.SH OPTIONS
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR \fB\-\-help\fR
show this help message and exit
.IP
Input/Output Options:
.TP
\fB\-f\fR \fB\-\-fin\fR FILENAME
Sequence input file (default: stdin)
.TP
\fB\-\-upload\fR URL
Upload input file from URL
.TP
\fB\-D\fR \fB\-\-datatype\fR FORMAT
Type of multiple sequence alignment or
position weight matrix file: (clustal, fasta,
msf, genbank, nbrf, nexus, phylip, stockholm,
intelligenetics, table, array, transfac)
.TP
\fB\-o\fR \fB\-\-fout\fR FILENAME
Output file (default: stdout)
.TP
\fB\-F\fR \fB\-\-format\fR FORMAT
Format of output: eps (default), png,
png_print, pdf, jpeg, svg, logodata
.IP
Logo Data Options:
.TP
\fB\-A\fR \fB\-\-sequence\-type\fR TYPE
The type of sequence data: 'protein', 'rna' or
\&'dna'.
.TP
\fB\-a\fR \fB\-\-alphabet\fR ALPHABET
The set of symbols to count, e.g. 'AGTC'. All
characters not in the alphabet are ignored. If
neither the alphabet nor sequence\-type are
specified then weblogo will examine the input
data and make an educated guess. See also
\fB\-\-sequence\-type\fR, \fB\-\-ignore\-lower\-case\fR
.TP
\fB\-U\fR \fB\-\-units\fR UNIT
A unit of entropy ('bits' (default), 'nats',
\&'digits'), or a unit offree energy ('kT',
\&'kJ/mol', 'kcal/mol'), or 'probability' for
probabilities
.TP
\fB\-\-composition\fR COMP.
The expected composition of the sequences:
\&'auto' (default), 'equiprobable', 'none' (do
not perform any compositional adjustment), a
CG percentage, a species name (e.g. 'E. coli',
\&'H. sapiens'), or an explicit distribution
(e.g. "{'A':10, 'C':40, 'G':40, 'T':10}"). The
automatic option uses a typical distribution
for proteins and equiprobable distribution for
everything else.
.TP
\fB\-\-weight\fR NUMBER
The weight of prior data.  Default depends on
alphabet length
.TP
\fB\-i\fR \fB\-\-first\-index\fR INDEX
Index of first position in sequence data
(default: 1)
.TP
\fB\-l\fR \fB\-\-lower\fR INDEX
Lower bound of sequence to display
.TP
\fB\-u\fR \fB\-\-upper\fR INDEX
Upper bound of sequence to display
.IP
Transformations:
.IP
Optional transformations of the sequence data.
.TP
\fB\-\-ignore\-lower\-case\fR
Disregard lower case letters and only count
upper case letters in sequences.
.TP
\fB\-\-reverse\fR
reverse sequences
.TP
\fB\-\-complement\fR
complement nucleic sequences
.TP
\fB\-\-revcomp\fR
reverse complement nucleic sequences
.IP
Logo Format Options:
.IP
These options control the format and display of the logo.
.TP
\fB\-s\fR \fB\-\-size\fR LOGOSIZE
Specify a standard logo size (small, medium
(default), large)
.TP
\fB\-n\fR \fB\-\-stacks\-per\-line\fR COUNT
Maximum number of logo stacks per logo line.
(default: 40)
.TP
\fB\-t\fR \fB\-\-title\fR TEXT
Logo title text.
.TP
\fB\-\-label\fR TEXT
A figure label, e.g. '2a'
.TP
\fB\-X\fR \fB\-\-show\-xaxis\fR YES/NO
Display sequence numbers along x\-axis?
(default: True)
.TP
\fB\-x\fR \fB\-\-xlabel\fR TEXT
X\-axis label
.TP
\fB\-\-annotate\fR TEXT
A comma separated list of custom stack
annotations, e.g. '1,3,4,5,6,7'.  Annotation
list must be same length as sequences.
.TP
\fB\-\-rotate\-numbers\fR YES/NO
Draw X\-axis numbers with vertical orientation
(default: False).
.TP
\fB\-\-number\-interval\fR NUMBER
Distance between numbers on X\-axis (default:
5)
.TP
\fB\-S\fR \fB\-\-yaxis\fR NUMBER
Height of yaxis in units. (Default: Maximum
value with uninformative prior.)
.TP
\fB\-Y\fR \fB\-\-show\-yaxis\fR YES/NO
Display entropy scale along y\-axis? (default:
True)
.TP
\fB\-y\fR \fB\-\-ylabel\fR TEXT
Y\-axis label (default depends on plot type and
units)
.TP
\fB\-E\fR \fB\-\-show\-ends\fR YES/NO
Label the ends of the sequence? (default:
False)
.TP
\fB\-P\fR \fB\-\-fineprint\fR TEXT
The fine print (default: weblogo version)
.TP
\fB\-\-ticmarks\fR NUMBER
Distance between ticmarks (default: 1.0)
.TP
\fB\-\-errorbars\fR YES/NO
Display error bars? (default: True)
.TP
\fB\-\-reverse\-stacks\fR YES/NO
Draw stacks with largest letters on top?
(default: True)
.IP
Color Options:
.IP
Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc
.TP
\fB\-c\fR \fB\-\-color\-scheme\fR SCHEME
Specify a standard color scheme (auto, base
pairing, charge, chemistry, classic,
hydrophobicity, monochrome)
.TP
\fB\-C\fR \fB\-\-color\fR COLOR SYMBOLS DESCRIPTION
Specify symbol colors, e.g. \fB\-\-color\fR black AG
\&'Purine' \fB\-\-color\fR red TC 'Pyrimidine'
.TP
\fB\-\-default\-color\fR COLOR
Symbol color if not otherwise specified.
.IP
Font Format Options:
.IP
These options provide control over the font sizes and types.
.TP
\fB\-\-fontsize\fR POINTS
Regular text font size in points (default: 10)
.TP
\fB\-\-title\-fontsize\fR POINTS
Title text font size in points (default: 12)
.TP
\fB\-\-small\-fontsize\fR POINTS
Small text font size in points (default: 6)
.TP
\fB\-\-number\-fontsize\fR POINTS
Axis numbers font size in points (default: 8)
.TP
\fB\-\-text\-font\fR FONT
Specify font for labels (default: ArialMT)
.TP
\fB\-\-logo\-font\fR FONT
Specify font for logo (default: Arial\-BoldMT)
.TP
\fB\-\-title\-font\fR FONT
Specify font for title (default: ArialMT)
.IP
Advanced Format Options:
.IP
These options provide fine control over the display of the logo.
.TP
\fB\-W\fR \fB\-\-stack\-width\fR POINTS
Width of a logo stack (default: 10.8)
.TP
\fB\-\-aspect\-ratio\fR POINTS
Ratio of stack height to width (default: 5)
.TP
\fB\-\-box\fR YES/NO
Draw boxes around symbols? (default: no)
.TP
\fB\-\-resolution\fR DPI
Bitmap resolution in dots per inch (DPI).
(Default: 96 DPI, except png_print, 600 DPI)
Low resolution bitmaps (DPI<300) are
antialiased.
.TP
\fB\-\-scale\-width\fR YES/NO
Scale the visible stack width by the fraction
of symbols in the column?  (I.e. columns with
many gaps of unknowns are narrow.)  (Default:
yes)
.TP
\fB\-\-debug\fR YES/NO
Output additional diagnostic information.
(Default: False)
.TP
\fB\-\-errorbar\-fraction\fR NUMBER
Sets error bars display proportion (default:
0.9)
.TP
\fB\-\-errorbar\-width\-fraction\fR NUMBER
Sets error bars width display proportion
(default: 0.25)
.TP
\fB\-\-errorbar\-gray\fR NUMBER
Sets error bars' gray scale percentage
(default: 0.75)
.IP
WebLogo Server:
.IP
Run a standalone webserver on a local port.
.TP
\fB\-\-serve\fR
Start a standalone WebLogo server for creating
sequence logos.
.TP
\fB\-\-port\fR PORT
Listen to this local port. (Default: 8080)