WEBLOGO(1)

✨ WEBLOGO(1) ✨

okay bestie, welcome to the weblogo manual page — it lives in the User Commands section of the manual, and it is literally the moment your sequence alignment becomes a look. 💅

---

💖 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. That's the whole vibe. You feed it an alignment, it gives you the aesthetic. 🎀

---

✨ OPTIONS ✨

• --version — show the program's version number and then dip. 👋
• -h, --help — show this help message and exit. ur little guide, fr.

🍓 Input/Output Options

• -f, --fin FILENAME — sequence input file (default: stdin)
• --upload URL — upload the input file straight from a URL 🌈
• -D, --datatype FORMAT — the type of multiple sequence alignment or position weight matrix file. ur options are: clustal, fasta, msf, genbank, nbrf, nexus, phylip, stockholm, intelligenetics, table, array, transfac
• -o, --fout FILENAME — output file (default: stdout)
• -F, --format FORMAT — format of the 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 get ignored, no cap. 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 of free 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. glow-up time.

• --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. this is where the main character energy happens 💅

• -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. micro-adjusting, but make it fashion.

• -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. ur own lil server, iconic.

• --serve — start a standalone WebLogo server for creating sequence logos.
• --port PORT — listen to this local port. (Default: 8080)

---

💡 quick reminder bestie: everything above is exactly what the page says — no extra lore, no invented behaviour. If it's not written here, weblogo never told us. 🫶

---

and that's the whole page, fr fr. This was WebLogo version 3.9.0, dated January 2026, living its life as WEBLOGO(1). slay, you read the entire manual 💖✨🎀🦋🌸💅