extract_specific_sites_from_msa

1 Introduction

extract_specific_sites_from_msa is a tool to extract some sites (or codon) from a multiple sequence alignment.

2 Installation

pip install extract_specific_sites_from_msa

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

3 Usage

usage: extract_specific_sites_from_msa [-h] [-infile <file>]
                                       [-format {fasta,emboss,stockholm,phylip,phylip-relaxed,clustal}]
                                       [-outformat {fasta,emboss,stockholm,phylip,phylip-relaxed,clustal}]
                                       [-outfile <file>] [-config <file>]
                                       [-codon <int>]

To extract some sites (or codon) from a multiple sequence alignment. By
Guanliang MENG, go to
https://github.com/linzhi2013/extract_specific_sites_from_msa for more
details.

optional arguments:
  -h, --help            show this help message and exit
  -infile <file>        input multiple sequence alignment file
  -format {fasta,emboss,stockholm,phylip,phylip-relaxed,clustal}
                        input file format [phylip-relaxed]
  -outformat {fasta,emboss,stockholm,phylip,phylip-relaxed,clustal}
                        output file format [fasta]
  -outfile <file>       outfile
  -config <file>        a file containing the sites to be extracted (1 left-
                        based). do not support 2-5, you should write 2 3 4 5
                        instead, the site numbers in config can be on one line
                        or multiple lines.
  -codon <int>          codon site to be extracted [2]

4 Author

Guanliang MENG

5 Citation

Currently I have no plan to publish extract_specific_sites_from_msa. However, if you use this program in your analysis, or you "steal" the idea/codes of this program into your script, I should be one of the co-authors in your publication!!!

However, since extract_specific_sites_from_msa makes use of Biopython, you should cite it if you use extract_specific_sites_from_msa 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). https://doi.org/10.1093/bioinformatics/btp163

Please go to http://www.biopython.org/ for more details.