Background

Phylogenetic trees are hierarchical   structures used for representing the inter-relationships between biological   entities. They are the most common tool for representing evolution and are   essential to a range of fields across the life sciences. The manipulation of   phylogenetic trees—in terms of adding or removing tips—is often performed by   researchers not just for reasons of management but also for performing   simulations in order to understand the processes of evolution. Despite this,   the most common programming language among biologists, R, has few class   structures well suited to these tasks.

Results

We present an R package that contains a   new class, called TreeMan, for representing the phylogenetic tree. This class   has a list structure allowing phylogenetic trees to be manipulated more   efficiently. Computational running times are reduced because of the ready   ability to vectorise and parallelise methods. Development is also improved   due to fewer lines of code being required for performing manipulation   processes.

背景

系统发育树是用来表示生物体间相互关系的层次结构。它们是最解析进化常用的工具，对生命科学的一系列领域发挥着至关重要的作用。研究人员出于管理的原因，或为了理解进化的过程，进行进化模拟，经常对系统发生树进行添加或删除末梢（分类单元）的操作。尽管如此，生物学家中最常见的编程语言R，很少有适合这些任务的类结构。

结果

我们提供了一个R包，其中包含一个新的类，称为TreeMan，用于表示系统发生树。这个类有一个列表结构，可以更有效地操纵系统发生树。由于具备矢量化能力和并行计算方法，计算运行时间大为缩短。由于执行操作过程所需的代码行更少，开发也得到了改进。