Getting trees into R : Trees in R are usually stored in the S3 phylo class   (implemented in ape), though the S4 phylo4 class (implemented in phylobase) is also available. ape can read trees from external files in newick format   (sometimes popularly known as phylip format) or NEXUS format. It can also   read trees input by hand as a newick string (i.e.,   "(human,(chimp,bonobo));"). phylobase and its lighter weight sibling rnclcan use the Nexus Class Library to read NEXUS, Newick, and other tree formats. treebase can search for and load trees from the online tree   repository TreeBASE, rdryad can pull data from the online data repository Dryad. RNeXML can read, write, and process metadata for the NeXML format. PHYLOCH can load trees from BEAST, MrBayes, and   other phylogenetics programs (PHYLOCH is only available from the author's website ).phyext2 can read and write various tree formats, including   simmap formats. rotl can pull in a synthetic tree and individual study   trees from the Open Tree of Life project. The treeio package can read trees in Newick, Nexus, New   Hampshire eXtended format (NHX), jplace and Phylip formats and data output   from BEAST, EPA, HyPhy, MrBayes, PAML, PHYLDOG, pplacer, r8s, RAxML and   RevBayes. phylogram can convert Newick files into dendrogram objects. brranching can fetch phylogenies from online repositories,   including phylomatic .

将系统发育树输入R中：R中的树通常存储在S3类数据Phylon类（在ape包中实现）中，而S4类数据Phylon4类（在phylobase包中实现）也可用。ape可读取newick格式（有时被普遍称为phylip格式）或nexus格式的外部文件树。它还可以将手工输入的newick格式字符串读取为树（如"(human,(chimp,bonobo));"）。phylobase及其重量较轻的兄弟rncl可以使用Nexus类库读取Nexus、Newick和其他格式树文件。treebase可以从在线树存储库TreeBASE中搜索和加载树，rdryad可以从在线数据库Dryad中提取数据。RNeXML可以读取、输出和处理NeXML格式的大数据。PHYLOCH可以从BEAST、MrBayes和其他系统发育学程序加载树（PHYLOCH只能从作者的网站上获得）。phyext2可以读写各种格式树文件，包括simmap格式。rotl可以从生命之树开放项目中引入合成树和单独研究树。treeio包可以读取Newick，Nexus，New Hampshire   eXtended（NHX）、jplace和Phylip等格式的树文件，以及由BEAST, EPA, HyPhy, MrBayes, PAML, PHYLDOG, pplacer, r8s, RAxML and   RevBayes等程序输出的数据。phylogram可以将Newick文件转换成dendrogram对象。brranching可以从在线数据库中获取系统发育树，包括phylomatic。