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To convert multiple alignment sequences (msa) to different format

Project description


1 Introduction

msaconverter is a tool to convert a multiple sequence alignment into different format with Biopython (

2 Installation

pip install msaconverter

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

3 Usage

$ msaconverter usage: [-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}]

Convert multiple-sequence-alignment into different formats. See 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]


Guanliang MENG


Currently I have no plan to publish msaconverter.

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).

Please go to for more details.

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