pegi3s/kakscalculator repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of KaKs Calculator⁠, a toolbox that calculates nonsynonymous (Ka) and synonymous (Ks) substitution rates by means of various models or model selection and averaging.

⁠Using the KaKs Calculator image in Linux

You should adapt and run the following commands:

• starting from FASTA file: docker run --rm -v /your/data/dir:/data pegi3s/kakscalculator bash -c "FASTA-AXT /data/input.fa && KaKs_Calculator -i /data/input.fa.axt -o /data/result.axt.kaks"

• starting from AXT file: docker run --rm -v /your/data/dir:/data pegi3s/kakscalculator bash -c "KaKs_Calculator -i /data/input.axt -o /data/result.axt.kaks"

In this commands, you should replace:

• /your/data/dir to point to the directory that contains the input file you want to process.
• input.fa to the actual name of your input file with the aligned CDS sequences (with no sequence line breaks) in FASTA format. The first nucleotide must correspond to the first codon position.
• input.axt to the actual name of your input file with the aligned CDS sequences in AXT format. The first nucleotide must correspond to the first codon position.

To see the KaKs Calculator help, just run docker run --rm pegi3s/kakscalculator bash -c "KaKs_Calculator -h".

⁠Note

In order to compile the KaKs Calculator software for Ubuntu, the following change was performed to the original file:

• added #include <string.h> to the top of base.h.