manavalang / mismatch_analyzer

Analyzes residue conservation in multiple sequence alignment.

Mismatch Analyzer

Analyzes residue conservation in multiple sequence alignment.

How to use?

1. Clone/download the repository
2. Run tool 'src/mismatch_analyzer' with appropriate arguments. For example:

cd src
python mismatch_analyzer.py -r ../data/reference.fasta  -qs ../data/query.fasta -qp "5,10,15"

3. Required arguments:

   • A reference sequence file
   • A query sequences file OR a pre-aligned MSA file
   • Query residue positions

4. To see arguments available, refer to help

python mismatch_analyzer.py -h

By default, output files would be written under directory output in directory with query sequences file or alignment file, depending on the input arguments used.

Requirements

• Python 2.7
• Required Python modules are listed in requirements.txt
• Clustal Omega if performing MSA is desired.

Example output

See following files for output produced by this tool.

1. CSV output
2. HTML output

License

Data and code in this repository is licensed under MIT license.