Galaxy | Tool Preview

Note

This tool uses CodonLogo in Galaxy to generate a sequence logo from a provided alignment. The input file must be an alignment in your current history. The tool will attempt to read a provided file and if it is unable to it will generate an error.

A typical output looks like this

/repository/static/images/253e22fdaf6a52c1/.%2Fstatic%2Fimages%2FCodonLogoExample.png

Warning about input files

The program used by this tool will fail if your alignment files are not all the same length.

Fasta alignments from ClustalW Galaxy tool will work but many other fasta files may cause this tool to produce an error and fail - please do not file a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta sequences are the same length!

Files must first be converted to fasta format in order to be used with this tool.


The default colour scheme is based on associated amino acid types:

Polar positive H, K, R -Light Blue

Polar negative D, E -Red

Polar neutral S, T, N, Q -Green

Non-polar aliphatic A, V, L, I, M -Blue

Non-polar aromatic F, W, Y -Magenta P, G -Brown C -Yellow

Stop codons -Black

Attribution

This Galaxy wrapper was modified for CodonLogo by David Murphy and is based on the wrapper written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL