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
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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