多重配列アラインメントのフォーマットを変換する msaconverter

タイトルの通りツール。簡単に紹介します。

インストール

依存

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

#conda( link)
mamba install bioconda::msaconverter -y

#pip
pip install msaconverter

> msaconverter -h

usage: msaconverter [-h] [-i <INFILE>] [-o <OUTFILE>] [-p {fasta,clustal,stockholm,nexus,phylip,phylip-sequential,phylip-relaxed,phylip-sequential-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.

options:

-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,phylip-sequential-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]

実行方法

多重整列の入力フォーマットと出力フォーマット、配列のタイプを指定する。

msaconverter -i input.aln -o out.phy -p fasta -q phylip -t DNA

-i input msa file
-o 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]