Jane: a new tool for the cophylogeny reconstruction problem.
Jane: a new tool for the cophylogeny reconstruction problem.
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DOI：
10.1186/1748-7188-5-16
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发表时间：
2010-02-03
期刊：
影响因子：
--
通讯作者：
Libeskind-Hadas R
中科院分区：
文献类型：
--
作者：
Conow C;Fielder D;Ovadia Y;Libeskind-Hadas R
本文介绍了一个新的软件工具，称为简，用于研究历史协会的理论和实现。这个问题出现在寄生虫学（宿主和寄生虫的关联）、分子系统学（排序和基因的关联）和植物地理学（区域和排序的关联）中。根本的问题是，协调对树木的生物合理的事件和与这些事件相关的成本。针对此问题的现有软件工具既有优势也有局限性，本文介绍的新Jane工具提供了对现有工具进行补充的功能。Jane软件工具使用多项式时间动态规划算法结合遗传算法来找到非常好的，并且通常是最优的，甚至对于相对较大的树对也是如此。该工具允许用户提供有关宿主树和寄生树的丰富时序信息。此外，用户可以通过指定主机树中的区域和区域对之间的主机交换机的成本来限制主机交换机距离和指定多个主机交换机成本。Jane还提供了一个图形用户界面，允许用户交互式地对程序找到的解决方案进行修改。简被证明是一个有用的工具，cophylogenic重建。它的功能是对现有工具的补充，因此可能对寄生虫学、分子系统学和昆虫学领域的研究人员有用。
This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools. The Jane software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. Jane also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program. Jane is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography.
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