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To convert multiple alignment sequences (msa) to different format

Project description

msaconverter

1 Introduction

msaconverter is a tool to convert a multiple sequence alignment into different format with Biopython (http://www.biopython.org/)

2 Installation

install with bioconda

pip install msaconverter
# or using Bioconda
conda install msaconverter

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

3 Usage

$ msaconverter
usage: msaconverter.py [-h] [-i <INFILE>] [-o <OUTFILE>]
                       [-p {fasta,clustal,stockholm,nexus,phylip,phylip-sequential,phylip-relaxed,mauve,maf}]
                       [-q {fasta,clustal,stockholm,nexus,phylip,phylip-sequential,phylip-relaxed,mauve,maf}]
                       [-t {DNA,RNA,protein}]

Convert multiple-sequence-alignment into different formats. See
https://biopython.org/wiki/AlignIO for format introductions. By Guanliang
MENG.

optional arguments:
  -h, --help            show this help message and exit
  -i <INFILE>           input msa file
  -o <OUTFILE>          output msa file
  -p {fasta,clustal,stockholm,nexus,phylip,phylip-sequential,phylip-relaxed,mauve,maf}
                        input msa format [fasta]
  -q {fasta,clustal,stockholm,nexus,phylip,phylip-sequential,phylip-relaxed,mauve,maf}
                        input msa format [phylip-relaxed]
  -t {DNA,RNA,protein}  Molecule types [DNA]

4 Author

Guanliang MENG

5 Citation

Currently I have no plan to publish msaconverter, 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 msaconverter makes use of Biopython, you should cite it if you use msaconverter 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.

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