CodonAlign

Generates a codon-based alignment from an amino acid alignment and CDS sequences

Description

This simple tool takes an amino acid alignment and converts it to a codon alignment,
provided a list of in-frame CDS sequences that translate to the aligned amino acids.

Dependencies

It depends on Biopython libraries: AlignIO, SeqIO, Alphabet, and codonalign.
Installation of Biopython can be done through pip:

# for a system-wide install
pip install biopython
# or for a local install
pip install --user biopython

Installation

git clone https://github.com/santiagosnchez/CodonAlign.git
# or 
wget https://raw.githubusercontent.com/santiagosnchez/CodonAlign/master/CodonAlign.py

Running the code:

For the help message type:

python CodonAlign.py -h

An example would be:

python CodonAlign.py -p prot.aln.fas -c cds.fas -o cds.aln.fas

This example will save the output to a file and print a message to the screen.
Please note that codonalign is currently printing a warning to STDERR. This message can be avoided by using the -s or --stdout option:

python CodonAlign.py -p prot.aln.fas -c cds.fas -s 2> /dev/null 1> cds.aln.fas