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To extract some codon positions (1st, 2nd, 3rd) from a CDS alignment.

Project description


1 Introduction

extract-codon-alignment ( is a tool to extract some codon positions (1st, 2nd, 3rd) from a CDS alignment with Biopython (

2 Installation

$ pip install extract-codon-alignment
# or with Bioconda
conda install extract-codon-alignment

There will be a command extract_codon_alignment created under the same directory as your pip command.

3 Usage

$ extract_codon_alignment
usage: extract_codon_alignment [-h] --alignedCDS <file>
                               [--aln_format <format>]
                               [--codonPoses {1,2,3,12,13,23}] --outAln <file>

To extract some codon positions (1st, 2nd, 3rd) from a CDS alignment.

optional arguments:
  -h, --help            show this help message and exit
  --alignedCDS <file>   The CDS alignment.
  --aln_format <format>
                        the file format for the CDS alignment. Anything
                        accepted by BioPython is fine [fasta]
  --codonPoses {1,2,3,12,13,23}
                        Codon position(s) to be extracted [12]
  --outAln <file>       output file name


Guanliang MENG


Currently I have no plan to publish extract-codon-alignment.

However, since extract-codon-alignment makes use of Biopython, you should cite it if you use extract-codon-alignment in your work:

Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon: “Biopython: freely available Python tools for computational molecular biology and bioinformatics”. Bioinformatics 25 (11), 1422–1423 (2009).

Please go to for more details.

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