INDELible: a flexible simulator of biological sequence evolution.
INDELible: a flexible simulator of biological sequence evolution.
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DOI：
10.1093/molbev/msp098
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发表时间：
2009-08
影响因子：
10.7
通讯作者：
Yang Z
中科院分区：
文献类型：
--
作者：
Fletcher W;Yang Z
从分子序列数据重建系统发生的方法有很多，但已知的系统发生方法很少，无法用于检验其有效性。模拟仍然是测试系统发育推断方法准确性和鲁棒性的最重要方法。然而，目前的模拟程序是有限的，特别是关于模拟插入和删除的现实模型。我们实现了一个便携且灵活的应用程序，名为INDELible，通过模拟插入和删除（indels）以及替换来生成核苷酸，氨基酸和密码子序列数据。在不同的长度分布模型下对模型进行了仿真。该程序实现了丰富的替代模型，包括一般不受限制的模型和核苷酸替代的非平稳非均匀模型，混合和分配模型，说明位点之间的异质性，密码子模型，允许非同义/同义取代率比率在位点和分支之间变化。由于其许多独特的特性，INDELible应该可用于评估许多推断方法的性能，包括多序列比对，系统发育树推断，祖先序列或基因组重建。
Many methods exist for reconstructing phylogenies from molecular sequence data, but few phylogenies are known and can be used to check their efficacy. Simulation remains the most important approach to testing the accuracy and robustness of phylogenetic inference methods. However, current simulation programs are limited, especially concerning realistic models for simulating insertions and deletions. We implement a portable and flexible application, named INDELible, for generating nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. Indels are simulated under several models of indel-length distribution. The program implements a rich repertoire of substitution models, including the general unrestricted model and nonstationary nonhomogeneous models of nucleotide substitution, mixture, and partition models that account for heterogeneity among sites, and codon models that allow the nonsynonymous/synonymous substitution rate ratio to vary among sites and branches. With its many unique features, INDELible should be useful for evaluating the performance of many inference methods, including those for multiple sequence alignment, phylogenetic tree inference, and ancestral sequence, or genome reconstruction.
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
5.8
作者：
Arndt, PF;Hwa, T
通讯作者：
Hwa, T
影响因子：
56.9
作者：
HILLIS, DM;BULL, JJ;MOLINEUX, IJ
通讯作者：
MOLINEUX, IJ
影响因子：
3.9
作者：
GU, X;LI, WH
通讯作者：
LI, WH
影响因子：
10.7
作者：
Galtier, N;Gouy, M
通讯作者：
Gouy, M