table of contents
| WEBLOGO(1) | User Commands | WEBLOGO(1) |
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¶
- 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
- 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)
| November 2022 | WebLogo 3.7.12 |