MutationCount

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.

Usage

• Example 1
• Example 2

Installation

LINUX

Open a terminal and use one of the following methods(Each line is a command you run in the terminal)

Clone and install

git clone https://github.com/VDBWRAIR/MutationCount.git
cd MutationCount
python setup.py install

If you don't have git

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

Requirements

Blast+

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 Packages

Python Requirements should be automatically fetched, but you may manually install them as well

Biopython numpy