SUMAC: Constructing Phylogenetic Supermatrices and Assessing Partially Decisive Taxon Coverage.
SUMAC: Constructing Phylogenetic Supermatrices and Assessing Partially Decisive Taxon Coverage.
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DOI：
10.4137/ebo.s35384
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发表时间：
2015
期刊：
影响因子：
--
通讯作者：
Freyman WA
中科院分区：
文献类型：
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作者：
Freyman WA
GenBank中的基因组信息序列数据量正以指数速度增长，大型系统发育树越来越多地用于研究。需要工具来从GenBank数据构建系统发育序列矩阵并评估缺失数据的影响。SUMAC是一种数据挖掘工具，用于构建系统发育超矩阵，并评估给定缺失序列数据模式的矩阵的系统发育决定性。SUMAC计算了一个新的度量，缺失序列决定性得分（MSDS），它衡量了每个缺失序列对矩阵决定性的贡献。MSDS可用于比较超矩阵并优先考虑新序列数据的获取。SUMAC构建超矩阵，通过一个分类组内的所有GenBank序列的探索性聚类，或通过使用指导序列以更有针对性的方式构建同源簇。SUMAC为GenBank中识别的任何分类组组装超矩阵，并通过并行化多个操作阶段来优化以在多核计算机系统上运行。SUMAC是作为一个Python包实现的，可以作为一个独立的命令行程序运行，或者它的模块和对象可以合并到其他程序中。SUMAC是在开源GPL v3许可下发布的，可在https://github.com/wf8/sumac上获得。
The amount of phylogenetically informative sequence data in GenBank is growing at an exponential rate, and large phylogenetic trees are increasingly used in research. Tools are needed to construct phylogenetic sequence matrices from GenBank data and evaluate the effect of missing data. Supermatrix Constructor (SUMAC) is a tool to data-mine GenBank, construct phylogenetic supermatrices, and assess the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. SUMAC calculates a novel metric, Missing Sequence Decisiveness Scores (MSDS), which measures how much each individual missing sequence contributes to the decisiveness of the matrix. MSDS can be used to compare supermatrices and prioritize the acquisition of new sequence data. SUMAC constructs supermatrices either through an exploratory clustering of all GenBank sequences within a taxonomic group or by using guide sequences to build homologous clusters in a more targeted manner. SUMAC assembles supermatrices for any taxonomic group recognized in GenBank and is optimized to run on multicore computer systems by parallelizing multiple stages of operation. SUMAC is implemented as a Python package that can run as a stand-alone command-line program, or its modules and objects can be incorporated within other programs. SUMAC is released under the open source GPLv3 license and is available at https://github.com/wf8/sumac.