SIMMAP: stochastic character mapping of discrete traits on phylogenies.
SIMMAP: stochastic character mapping of discrete traits on phylogenies.
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DOI：
10.1186/1471-2105-7-88
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发表时间：
2006-02-23
影响因子：
3
通讯作者：
Bollback JP
中科院分区：
文献类型：
--
作者：
Bollback JP
在我们对分子、形态和行为进化的理解中，遗传学上的特征映射发挥了重要的作用，如果不是关键的话。直到最近，我们一直依赖于简约来推断性格变化。吝啬有许多严重的局限性，这是我们理解的缺陷。最近的统计方法已经开发出来，使我们摆脱这些限制，使我们能够克服简约的问题，适应进化时间，祖先状态和遗传的不确定性。SIMMAP已经被开发用于实现随机特征映射，这对分子进化论者、系统论者和生物信息学家都很有用。研究人员可以解决有关正选择，氨基酸取代模式，性状关联和形态进化模式的问题。SIMMAP软件中实现的随机字符映射使用户能够使用不依赖于简约性的概率方法来解决需要将字符映射到随机性的问题。可以使用完全贝叶斯方法进行分析，该方法不依赖于考虑单个拓扑结构、替代模型参数集或祖先状态的重建。这些数量的不确定性是通过使用MCMC样本从各自的后验分布。
Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny. SIMMAP has been developed to implement stochastic character mapping that is useful to both molecular evolutionists, systematists, and bioinformaticians. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution. Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.
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影响因子：
6.5
作者：
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通讯作者：
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影响因子：
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作者：
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影响因子：
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通讯作者：
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DOI：
10.1073/pnas.97.10.5322
发表时间：
2000-05-09
影响因子：
11.1
作者：
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通讯作者：
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