氨基酸替代率估算程序
modelestimator-v2的Python项目详细描述
模型估计器---从MSA推断序列进化率矩阵
示例用法
modelestimator -t 0.001 file1.fa file2.fa file3.fa
从三个fasta格式的对齐文件中推断速率矩阵（写入stdout）。
modelestimator -b 200 file.fa
在fasta多重对齐上尝试实验性的引导功能（200个副本）。
语法
modelestimator <options> infiles
<format>应为fasta、斯德哥尔摩或phylip格式。
输出是一个速率矩阵和剩余分布向量。
选项
-h, --help show this help message and exit
--version show program's version number and exit
-a {iqtree,matlab,mrbayes,octave,paml,phyml}, --application {iqtree,matlab,mrbayes,octave,paml,phyml}
Choose output format to suit the application you want
to use for inference. The 'iqtree', 'paml' and 'phyml'
options are identical. The 'matlab' and 'octave'
optins are for import into MatLab-compatible programs
and are presenting the actual Q matrix rather than the
R matrix used by PAML/PhyML, etc. Default: paml
-f {fasta,clustal,nexus,phylip,stockholm}, --format {fasta,clustal,nexus,phylip,stockholm}
Specify sequence format of input files. Default: fasta
-t T, --threshold T Stop when consecutive iterations do not change by more
than T. Default: 0.001
-b N, --bootstrap N Estimate the rate matrix using bootstrapping by
computing N resampled replicates of the input
multialignment. For each replicate, a rate matrix is
computed. The mean matrix the elementwise standard
deviation is returned. Only one infile should be given
in this mode.
-B N, --bootstrapped_quality N
Estimate the quality of the rate matrix estimate using
a bootstrap procedure. The multialignment is resampled
N times and a Q matrix is computed for each replicate.
Then the difference (matrix norm) between rate matrix
estimated without resampling and each bootstrapped Q
is computed and the mean difference is returned. Only
one infile should be given in this mode. Returns
bootstrap norm.
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