Analyze spatial phylogenetic diversity patterns. 
    Use your data on an evolutionary tree and geographic distributions of the 
    terminal taxa to compute diversity and endemism metrics, test significance 
    with null model randomization, analyze community turnover and biotic 
    regionalization, and perform spatial conservation prioritizations. All 
    functions support quantitative community data in addition to binary data.

Functions to read and write APE-compatible phylogenetic
  trees in NEXUS and Newick formats, while preserving annotations.

Tools for calculating and viewing topological properties of phylogenetic trees.

Classification based analysis of DNA sequences to taxonomic groupings. This package primarily implements Naive Bayesian Classifier from the Ribosomal Database Project. This approach has traditionally been used to classify 16S rRNA gene sequences to bacterial taxonomic outlines; however, it can be used for any type of gene sequence. The method was originally described by Wang, Garrity, Tiedje, and Cole in Applied and Environmental Microbiology 73(16):5261-7 <doi:10.1128/AEM.00062-07>. The package also provides functions to read in 'FASTA'-formatted sequence data.

Analyzis and filtering of phylogenomics datasets. 
	It takes an input either a collection of gene trees (then transformed to matrices) or directly a collection of gene matrices and performs an iterative process to identify
	what species in what genes are outliers, and whose elimination significantly improves the concordance between the input matrices. The methods builds upon the Distatis approach (Abdi et al. (2005) <doi:10.1101/2021.09.08.459421>), a generalization of classical multidimensional scaling to multiple distance matrices.

A collection of functions to do model-based phylogenetic analysis. 
    It includes functions to calculate community phylogenetic diversity,
    to estimate correlations among functional traits while accounting for 
    phylogenetic relationships, and to fit phylogenetic generalized linear
    mixed models. The Bayesian phylogenetic generalized linear mixed models
    are fitted with the 'INLA' package (<https://www.r-inla.org>).