Diversification   Analysis: 

Lineage through time plots   can be done in ape; nLTT can   estimate the normalized lineage through time statistic, which can be used as   a summary statistic in ABC   approaches. A simple birth-death model for when you have extant species only (sensu   Nee et al. 1994) can be fitted in ape as can survival models and goodness-of-fit tests (as applied to   testing of models of diversification). TESS can   calculate the likelihood of a tree under a model with time-dependent   diversification, including mass extinctions. Net rates of diversification   (sensu Magellon and Sanderson) can be calculated in geiger.diversitree implements   the BiSSE method (Maddison et al. 1997) and later improvements (FitzJohn et   al. 2009). TreePar estimates   speciation and extinction rates with models where rates can change as a   function of time (i.e., at mass extinction events) or as a function of the   number of species. caper can   do the macrocaic test to evaluate the effect of a a trait on diversity. apTreeshape also   has tests for differential diversification (see description ). iteRates can   identify and visualize areas on a tree undergoing differential   diversification. DDD can   fit density dependent models as well as models with occasional escape from   density-dependence. BAMMtools is   an interface to the BAMM program to allow visualization of rate shifts,   comparison of diversification models, and other functions. DDD implements   maximum likelihood methods based on the diversity-dependent birth-death   process to test whether speciation or extinction are diversity-dependent, as   well as identifies key innovations and simulate a density-dependent   process. PBD can   calculate the likelihood of a tree under a protracted speciation model. phyloTop has functions for investigating   tree shape, with special functions and datasets relating to trees of   infectious diseases.

分化分析：

ape可以谱系随时间变化的图形；nLTT可以进行谱系的时间变化的标准化统计，从而汇总统计不同方法的结果。当你只有现存物种时（根据Nee   et al. 1994），一个简单的出生-死亡模型可以使用ape模拟，同时，可以用ape进行生存模型和拟合度测试（同多样化模型的测试）。TESS可以计算出一棵树在具有时间依赖的分化模型下的似然值，包括大规模灭绝。净分化速率（依据Magellon   and Sanderson）可用geiger计算。diversitree可运行BiSSE方法（Maddison   et al. 1997）并进行后续优化（FitzJohn   et al. 2009）。TreePar通过模型估计物种形成和灭绝速率，模型中的速率可以随时间（即大规模灭绝事件）或物种数量的变化而变化。caper可以做macrocaic测试来评估一个性状对多样性的影响。apTreeshape也有趋异分化检验（见说明）。iteRates可以识别和可视化系统发育树上正在经历趋异分化的区域。DDD既能拟合密度依赖模型，也能拟合偶尔脱离密度依赖的模型。BAMMtools是BAMM程序的一个接口，用于可视化速率变化、多样化模型比较和其他功能。DDD实现了基于多样性依赖的出生-死亡过程的最大似然方法，以检验物种形成或灭绝是否依赖于多样性，识别关键创新并模拟密度依赖过程。PBD可以计算一棵树在长时间物种形成模型下的可能性。phyloTop具有研究树形的功能，具有与传染病树相关的特殊功能和数据集。