1. 官网
https://github.com/marekborowiec/AMAS/
2. 安装
PIP安装:https://pypi.org/project/amas/
AMAS是一个
Python
模块,要求Python
版本为3.4
及以上
3. 查看帮助文件
python3 绝对路径/AMAS.py -h
usage: AMAS <command> [<args>]
The AMAS commands are:
concat Concatenate input alignments
convert Convert to other file format
replicate Create replicate data sets for phylogenetic jackknife
split Split alignment according to a partitions file
summary Write alignment summary
remove Remove taxa from alignment
translate Translate DNA alignment into protein alignment
trim Remove columns from alignment
Use AMAS <command> -h for help with arguments of the command of interest
positional arguments:
command Subcommand to run
optional arguments:
-h, --help show this help message and exit
4. convert
fasta, phylip, nexus, phylip-int, nexus-int物种文件格式之间的互相转换
(RStudio-5) zhiyong@zhiyong-OptiPlex-7050:~/Application/anaconda3/envs/RStudio-5/lib/python3.8/site-packages/amas$ AMAS.py convert -h
usage: AMAS.py [-h] [-u {fasta,phylip,nexus,phylip-int,nexus-int}] [-e] [-c CORES] -i IN_FILES [IN_FILES ...] -f {fasta,phylip,nexus,phylip-int,nexus-int} -d {aa,dna}
Convert to other file format
optional arguments:
-h, --help show this help message and exit
-u {fasta,phylip,nexus,phylip-int,nexus-int}, --out-format {fasta,phylip,nexus,phylip-int,nexus-int}
File format for the output alignment. Default: fasta
-e, --check-align Check if input sequences are aligned. Default: no check
-c CORES, --cores CORES
Number of cores used. Default: 1
required arguments:
-i IN_FILES [IN_FILES ...], --in-files IN_FILES [IN_FILES ...]
Alignment files to be taken as input. You can specify multiple files using wildcards (e.g. --in-files *fasta)
-f {fasta,phylip,nexus,phylip-int,nexus-int}, --in-format {fasta,phylip,nexus,phylip-int,nexus-int}
The format of input alignment
-d {aa,dna}, --data-type {aa,dna}
Type of data
4.1 将fasta
转换成phylip
python3 绝对路径/AMAS.py convert -d dna -f fasta -i alihment.fasta -u phylip
dna
: 输入文件的类型,aa
或者dna
-f
: 输入文件的格式
-i
: 输入文件的文件名
-u
: 输出文件的格式
输出文件的文件名由程序生成,即在输入文件的文件名后添加
-out.输出文件格式缩写
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