#Alignment-Handler Performs codon alignment by using muscle/mafft package. It automatically identifies a correct frame to perform codon alignment.
##Instructions Use
python align.py -i inputFileName -itype inputAlignMentType -o OutPutFileName -otype outputAlignMentType
You can choose to ignore stop codon check using -ign argument.
python align.py -i inputFileName -itype inputAlignMentType -o OutPutFileName -otype outputAlignMentType -ign
####Handling low quality CDS Several coding sequences contains in-frame stop codons and are considered as low quality sequences. Alignment-Handler '-omit' argument screens these sequences and omits it from the alignment dataset.
python align.py -i inputFileName -itype inputAlignMentType -o OutPutFileName -otype outputAlignMentType -omit
Use "python align.py -h" to know more about argument types.