Count Mutations between a reference sequence and aligned sequences
Based on a given reference(--subject) sequence file, align all query sequences to that subject and count the differences in the alignment.
Blastn seems to be the fastest way to do these quick alignments so it is attempted first. If it fails then t_coffee is used.
Open a terminal and use one of the following methods(Each line is a command you run in the terminal)
git clone https://github.com/VDBWRAIR/MutationCount.git
cd MutationCount
python setup.py install
pushd /tmp
wget https://github.com/VDBWRAIR/MutationCount/archive/master.zip -O MutationCount.zip
unzip MutationCount.zip
cd MutationCount-master
python setup.py install
popd
You need to install the Blast+ package http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download After it is installed you will need to ensure that blastn is included in your environment's path
Python Requirements should be automatically fetched, but you may manually install them as well
Biopython numpy