Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France.
Inria Grenoble, Montbonnot 38334, France.
Bioinformatics. 2020 Aug 15;36(14):4197-4199. doi: 10.1093/bioinformatics/btaa498.
Phylogenetic tree reconciliation is the method of choice in analyzing host-symbiont systems. Despite the many reconciliation tools that have been proposed in the literature, two main issues remain unresolved: (i) listing suboptimal solutions (i.e. whose score is 'close' to the optimal ones) and (ii) listing only solutions that are biologically different 'enough'. The first issue arises because the optimal solutions are not always the ones biologically most significant; providing many suboptimal solutions as alternatives for the optimal ones is thus very useful. The second one is related to the difficulty to analyze an often huge number of optimal solutions. In this article, we propose Capybara that addresses both of these problems in an efficient way. Furthermore, it includes a tool for visualizing the solutions that significantly helps the user in the process of analyzing the results.
The source code, documentation and binaries for all platforms are freely available at https://capybara-doc.readthedocs.io/.
yishu.wang@univ-lyon1.fr or blerina.sinaimeri@inria.fr.
Supplementary data are available at Bioinformatics online.
系统发育树协调是分析宿主-共生体系统的首选方法。尽管文献中已经提出了许多协调工具，但仍存在两个未解决的主要问题：（i）列出次优解决方案（即得分“接近”最优解决方案的解决方案）和（ii）仅列出足够“不同”的生物学差异的解决方案。第一个问题是因为最优解决方案并不总是生物学上最重要的解决方案；因此，提供许多次优解决方案作为最优解决方案的替代方案非常有用。第二个问题与分析通常数量庞大的最优解决方案的难度有关。在本文中，我们提出了 Capybara，它以有效的方式解决了这两个问题。此外，它还包含一个用于可视化解决方案的工具，这极大地帮助了用户在分析结果的过程中。
所有平台的源代码、文档和二进制文件均可在 https://capybara-doc.readthedocs.io/ 免费获取。
yishu.wang@univ-lyon1.fr 或 blerina.sinaimeri@inria.fr。
补充数据可在生物信息学在线获得。
Zotero 插件