WebLogo is a tool for generating sequence logos, which are graphical representations of patterns in multiple sequence alignments. Sequence logos provide a more detailed and accurate description of sequence similarity compared to consensus sequences. Each logo consists of stacks of letters, with the height of each stack indicating the conservation of the sequence at that position, measured in bits. The height of individual symbols reflects the frequency of the corresponding amino acid or nucleotide at that position. WebLogo allows users to generate sequence logos for RNA, DNA, or protein alignments in FASTA or CLUSTAL formats. It also provides a command line interface and open-source code for local installation and customization. Sequence logos were developed by Tom Schneider and Mike Stephens to display patterns in sequence conservation and assist in discovering and analyzing these patterns. They have been used to analyze DNA-binding sites, protein structures, and other biological sequences. WebLogo can also display error bars to indicate sampling errors. The colors of the symbols in the logos are determined by their chemical properties, and users can customize the coloring scheme. WebLogo can generate output in various graphic formats, including GIF, PNG, EPS, and PDF. The website is freely available, and users can run WebLogo on a local server with a command line interface. The tool is supported by grants from the NIH and the Searle Scholars program. The publication costs were partially covered by page charges, and the article is marked as an advertisement. The tool has been cited in numerous studies and is widely used in bioinformatics.WebLogo is a tool for generating sequence logos, which are graphical representations of patterns in multiple sequence alignments. Sequence logos provide a more detailed and accurate description of sequence similarity compared to consensus sequences. Each logo consists of stacks of letters, with the height of each stack indicating the conservation of the sequence at that position, measured in bits. The height of individual symbols reflects the frequency of the corresponding amino acid or nucleotide at that position. WebLogo allows users to generate sequence logos for RNA, DNA, or protein alignments in FASTA or CLUSTAL formats. It also provides a command line interface and open-source code for local installation and customization. Sequence logos were developed by Tom Schneider and Mike Stephens to display patterns in sequence conservation and assist in discovering and analyzing these patterns. They have been used to analyze DNA-binding sites, protein structures, and other biological sequences. WebLogo can also display error bars to indicate sampling errors. The colors of the symbols in the logos are determined by their chemical properties, and users can customize the coloring scheme. WebLogo can generate output in various graphic formats, including GIF, PNG, EPS, and PDF. The website is freely available, and users can run WebLogo on a local server with a command line interface. The tool is supported by grants from the NIH and the Searle Scholars program. The publication costs were partially covered by page charges, and the article is marked as an advertisement. The tool has been cited in numerous studies and is widely used in bioinformatics.