Implements novel tools for estimating sample sizes needed for phylogenetic studies, including
    studies focused on estimating the probability of true pathogen transmission between two cases given phylogenetic linkage and studies focused on tracking pathogen variants at a population level. Methods described in Wohl, Giles, and Lessler (2021) and in Wohl, Lee, DiPrete, and Lessler (2023).

Applies phylogenetic comparative methods (PCM) and phylogenetic trait imputation using 
    structural equation models (SEM), extending methods from Thorson et al. (2023) <doi:10.1111/2041-210X.14076>.  
    This implementation includes a minimal set of features, to 
    allow users to easily read all of the documentation and source code.  PCM using SEM 
    includes phylogenetic linear models and structural equation models as nested submodels, 
    but also allows imputation of missing values.  Features and comparison with other packages
    are described in Thorson and van der Bijl (2023) <doi:10.1111/jeb.14234>.

Provides functions for graph-based multiple-sample
    testing and visualization of microbiome data, in particular data
    stored in 'phyloseq' objects. The tests are based on those
    described in Friedman and Rafsky (1979)
    <http://www.jstor.org/stable/2958919>, and the tests are described
    in more detail in Callahan et al. (2016)
    <doi:10.12688/f1000research.8986.1>.

A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.

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

A collection of tools for building RAxML supermatrix using
             PHYLIP or aligned FASTA files. These functions will be
             useful for building large phylogenies using multiple markers.