msaconverter

THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

WHEN YOU ADAPT (PART OF) THE SOFTWARE FOR YOUR USE CASES, THE AUTHOR AND THE SOFTWARE MUST BE EXPLICITLY CREDITED IN YOUR PUBLICATIONS AND SOFTWARE, AND YOU SHOULD ASK THE USERS OF YOUR SOFTWARE TO CITE THE SOFTWARE IN THEIR PUBLICATIONS. IN A WORD, 请讲武德.

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,phylip-sequential-relaxed,mauve,maf}]
                   [-t {DNA,RNA,protein}]

THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY
AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM
LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
PERFORMANCE OF THIS SOFTWARE.

**WHEN YOU ADAPT (PART OF) THE SOFTWARE FOR YOUR USE CASES, THE AUTHOR AND
THE SOFTWARE MUST BE EXPLICITLY CREDITED IN YOUR PUBLICATIONS AND SOFTWARE,
AND YOU SHOULD ASK THE USERS OF YOUR SOFTWARE TO CITE THE SOFTWARE IN
THEIR PUBLICATIONS. IN A WORD, 请讲武德.**

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

V0.0.3:
phylip-sequential-relaxed (for output) is a custom format by MGL, which
allows long sequence names but like phylip-sequential.

By Guanliang MENG, available from https://github.com/linzhi2013/msaconverter.

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,phylip-sequential-relaxed,mauve,maf}
                        input msa format [phylip-relaxed]
  -t {DNA,RNA,protein}  Molecule types [DNA]

4 Author

Guanliang MENG

5 Citation

You should cite this repository when you use msaconverter in your project.

Since msaconverter makes use of Biopython, you should also cite it at the same time:

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.