ambuj-uf / alignment-handler Goto Github PK

#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.