ADOMA is a command line (Linux) tool that modifies the graphical output of clustalW multiple sequence alignments. Especially when sequences are very similar, (e.g., when only small differences such as SNPs are present), ADOMA can help to make visualization easier. Furthermore, it can color the residues in the sequence alignments. ADOMA works both with DNA or protein sequences.
ADOMA is easily integrated in automatic (NGS) analysis pipelines, and therefore manual handling with sequencing files or importing to GUI tools are not necessary. It produces direct easily interpretable output in HTML or text format. ADOMA is written in bash and python and is freely available at:
http://sourceforge.net/projects/adoma/
Read more about ADOMA in Molecular Informatics:
http://onlinelibrary.wiley.com/doi/10.1002/minf.201500083/abstract
How to cite ADOMA:
Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. Mol. Inf., 35: 42-44. doi: 10.1002/minf.201500083
