--- name: "weblogo" section: "1" platform: "linux" package: "python3-weblogo" version: "3.8.0-2" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/weblogo" --- # weblogo(1) create sequence logos from biological sequence alignments ## NAME WebLogo - create sequence logos from biological sequence alignments ## SYNOPSIS **weblogo** \[*options*\] *\< sequence\_data.fa \> sequence\_logo.eps* ## DESCRIPTION Create sequence logos from biological sequence alignments. ## OPTIONS - **--version** show program's version number and exit - **-h** **--help** show this help message and exit - Input/Output Options: - **-f** **--fin** FILENAME Sequence input file (default: stdin) - **--upload** URL Upload input file from URL - **-D** **--datatype** FORMAT Type of multiple sequence alignment or position weight matrix file: (clustal, fasta, msf, genbank, nbrf, nexus, phylip, stockholm, intelligenetics, table, array, transfac) - **-o** **--fout** FILENAME Output file (default: stdout) - **-F** **--format** FORMAT Format of output: eps (default), png, png\_print, pdf, jpeg, svg, logodata, csv - Logo Data Options: - **-A** **--sequence-type** TYPE The type of sequence data: 'protein', 'rna' or 'dna'. - **-a** **--alphabet** 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 **--sequence-type**, **--ignore-lower-case** - **-U** **--units** UNIT A unit of entropy ('bits' (default), 'nats', 'digits'), or a unit offree energy ('kT', 'kJ/mol', 'kcal/mol'), or 'probability' for probabilities - **--composition** 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. - **--weight** NUMBER The weight of prior data. Default depends on alphabet length - **-i** **--first-index** INDEX Index of first position in sequence data (default: 1) - **-l** **--lower** INDEX Lower bound of sequence to display - **-u** **--upper** INDEX Upper bound of sequence to display - Transformations: - Optional transformations of the sequence data. - **--ignore-lower-case** Disregard lower case letters and only count upper case letters in sequences. - **--reverse** reverse sequences - **--complement** complement nucleic sequences - **--revcomp** reverse complement nucleic sequences - Logo Format Options: - These options control the format and display of the logo. - **-s** **--size** LOGOSIZE Specify a standard logo size (small, medium (default), large) - **-n** **--stacks-per-line** COUNT Maximum number of logo stacks per logo line. (default: 40) - **-t** **--title** TEXT Logo title text. - **--label** TEXT A figure label, e.g. '2a' - **-X** **--show-xaxis** YES/NO Display sequence numbers along x-axis? (default: True) - **-x** **--xlabel** TEXT X-axis label - **--annotate** 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. - **--rotate-numbers** YES/NO Draw X-axis numbers with vertical orientation (default: False). - **--number-interval** NUMBER Distance between numbers on X-axis (default: 5) - **-S** **--yaxis** NUMBER Height of yaxis in units. (Default: Maximum value with uninformative prior.) - **-Y** **--show-yaxis** YES/NO Display entropy scale along y-axis? (default: True) - **-y** **--ylabel** TEXT Y-axis label (default depends on plot type and units) - **-E** **--show-ends** YES/NO Label the ends of the sequence? (default: False) - **-P** **--fineprint** TEXT The fine print (default: weblogo version) - **--ticmarks** NUMBER Distance between ticmarks (default: 1.0) - **--errorbars** YES/NO Display error bars? (default: True) - **--reverse-stacks** YES/NO Draw stacks with largest letters on top? (default: True) - Color Options: - Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc - **-c** **--color-scheme** SCHEME Specify a standard color scheme (auto, base pairing, charge, chemistry, classic, hydrophobicity, monochrome) - **-C** **--color** COLOR SYMBOLS DESCRIPTION Specify symbol colors, e.g. **--color** black AG 'Purine' **--color** red TC 'Pyrimidine' - **--default-color** COLOR Symbol color if not otherwise specified. - Font Format Options: - These options provide control over the font sizes and types. - **--fontsize** POINTS Regular text font size in points (default: 10) - **--title-fontsize** POINTS Title text font size in points (default: 12) - **--small-fontsize** POINTS Small text font size in points (default: 6) - **--number-fontsize** POINTS Axis numbers font size in points (default: 8) - **--text-font** FONT Specify font for labels (default: ArialMT) - **--logo-font** FONT Specify font for logo (default: Arial-BoldMT) - **--title-font** FONT Specify font for title (default: ArialMT) - Advanced Format Options: - These options provide fine control over the display of the logo. - **-W** **--stack-width** POINTS Width of a logo stack (default: 10.8) - **--aspect-ratio** POINTS Ratio of stack height to width (default: 5) - **--box** YES/NO Draw boxes around symbols? (default: no) - **--resolution** DPI Bitmap resolution in dots per inch (DPI). (Default: 96 DPI, except png\_print, 600 DPI) Low resolution bitmaps (DPI\<300) are antialiased. - **--scale-width** 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) - **--debug** YES/NO Output additional diagnostic information. (Default: False) - **--errorbar-fraction** NUMBER Sets error bars display proportion (default: 0.9) - **--errorbar-width-fraction** NUMBER Sets error bars width display proportion (default: 0.25) - **--errorbar-gray** NUMBER Sets error bars' gray scale percentage (default: 0.75) - WebLogo Server: - Run a standalone webserver on a local port. - **--serve** Start a standalone WebLogo server for creating sequence logos. - **--port** PORT Listen to this local port. (Default: 8080)