For the lastest version of the pipeline, please go to: https://github.com/lyy005/codon_alignment/releases

• Performing codon alignment for coding sequences (CDS)
• Unaligned coding sequences are the only input needed (if using default universal codon table or invertebrate codon table)
• Multiple alignment with MAFFT (executable mafft-linsi file needs to be added to current directory)
• Customized the threshold for the percentage of non-gap basepairs in a multiple sequence alignment
• Two codon tables are supported: 1 - for The Standard Genetic Code; 5 - for The Invertebrate Mitochondrial Genetic Code
• Details about codon tables please refer to https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

Li, Y., Zhang, R., Liu, S., Donath, A., Peters, R.S., Ware, J., Misof, B., Niehuis, O., Pfrender, M.E. and Zhou, X., 2017. The molecular evolutionary dynamics of oxidative phosphorylation (OXPHOS) genes in Hymenoptera. BMC evolutionary biology, 17(1), p.269.

• Download MAFFT (https://mafft.cbrc.jp/alignment/software/) and added the executable file mafft-linsi to current directory (i.e. codon_alignment directory).

perl codon_alignment.pl [cds fas] [codon table id] [minimum coverage]

• [cds fas] CDS sequences in fasta format
• [codon table id] 1 for Standard Code, 5 for Invertebrate Mitochondrial Code
• [minimum coverage] Minimum coverage of non-gap basepairs in the multiple alignment (range from 0 to 1). For example: 0.7 means sequences after the first round of multiple sequence alignment should have >= 70% of non-gap basepairs

• Go to the example file directory

   cd ./examples
  

• Make multiple sequence alignments based on COX1 gene (mitochondrial codon table) and remove the sequences with < 70% non-gap basepairs

   ../codon_alignment.pl COX1.fasta 5 0.7
  

Li, Y., Zhang, R., Liu, S., Donath, A., Peters, R.S., Ware, J., Misof, B., Niehuis, O., Pfrender, M.E. and Zhou, X., 2017. The molecular evolutionary dynamics of oxidative phosphorylation (OXPHOS) genes in Hymenoptera. BMC evolutionary biology, 17(1), p.269.

Katoh, K., and Standley, D.M., 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution 30(4), p.772-780.