MSA4U is a simple visualisation tool for Multiple Sequence Alignments.

Input format: Multiple sequence alignments or unaligned sequences in fasta format.
Output: MSA plot in vector format (pdf)
In case of unaligned sequences as input msa4u uses MAFFT with --auto option to build MSA.

Source code and documentation are available at the GitHub Page.

Output example


If you find msa4u useful, please cite uorf4u paper. msa4u initially was developed as a sublibrary of uorf4u.
Artyom A. Egorov, Gemma C. Atkinson, uORF4u: a tool for annotation of conserved upstream open reading frames Bioinformatics, Volume 39, Issue 5, May 2023, btad323; doi: 10.1093/bioinformatics/btad323

Authors & Contact

msa4u is developed by Artyom Egorov at the Atkinson Lab.
We are open for suggestions of how we can extend and improve msa4u functionality. Please don't hesitate to share your ideas or feature requests.

Please contact us by e-mail or use GitHub Issues to report any technical problems related to msa4u. You can also use Discussions section for sharing your ideas or feature requests!

Submission form

You can try an example with several protein sequences.

Mandatory arguments
Select only one*of the allowed input formats.
Demo fasta file was successfully uploaded.
Fasta file with unaligned sequences.
File format: .fa or .fasta;
Fasta file with multiple sequence alignments.
File format: .fa or .fasta;
Optional arguments
Part of sequences' header to use as labels
Fasta' header style:
>sequence_id after first space description starts
Configuration file to replace the default one.
Use the premade config file as a template: Standard
Palette file to replace the default one.
Use the premade palette file as a template: Palette
Color code for your sequence.
Use the premade color code files as a template: Colors aa, Colors nt
Run parameters
Please, enter your e-mail address to receive your results link.
Will be used in output folder name. If set Default then basename of your input file will be used.