Description: Functions to read and write APE-compatible phylogenetic
trees in NEXUS and Newick formats, while preserving annotations.
Collate: 'utility.R' 'tokenize.R' 'newick.R' 'nexus.R' 'format.R'

Author: Daniel Beer [aut], Anusha Beer [aut]

Title: Phylogenetic tools for ecologists
Author: Jinlong Zhang, Xiangcheng Mi, Nancai Pei
Description: Tools for phylogenetic analysis espetially for DNA
Packaged: 2010-10-22 23:37:23 UTC; Administrator

Description: Tools for manupulating DNA sequences for DNA-barcoding,
Packaged: 2010-11-01 12:34:53 UTC; Administrator

Title: Phylogenetic tools for Eco-phylogenetics
Author: Jinlong Zhang, Nancai Pei, Xiangcheng Mi
Description: Building supermatrix for DNA barcodes using different
genes, calculating the inequality among lineages and
phylogenetic similarity for very large dataset using slicing
Depends: seqRFLP, ape, picante, spaa, fields
Packaged: 2011-07-20 19:28:12 UTC; Administrator

Title: Phylogenetic Tools for Eco-Phylogenetics
Authors@R: c(person("Jinlong", "Zhang", role = c("aut", "cre"), email = "jinlongzhang01@gmail.com"),
person("Nancai", "Pei", role = c("ctb")),
person("Xiangcheng", "Mi", role = c("ctb")))
Description: 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.

Description: Use topological or taxonomic information to maximize the overlap of phylogenetic and comparative data.
Author: Rich FitzJohn, Matt Pennell and Will Cornwell
Packaged: 2015-08-12 20:29:34 UTC; mwpennell

Title: Model Based Phylogenetic Analysis
person("Anthony", "Ives", , "arives@wisc.edu", role = c("aut")),
person("Russell", "Dinnage", , "r.dinnage@gmail.com", role = c("aut"), comment = c(ORCID = "0000-0003-0846-2819")),
person(c("Lucas", "A."), "Nell", , "lucas@lucasnell.com", role = c("aut"), comment = c(ORCID = "0000-0003-3209-0517")),
person("Matthew", "Helmus", , "mrhelmus@temple.edu", role = c("aut")),
person("Daijiang", "Li", , "daijianglee@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0925-3421")))
Description: 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 (<http://www.r-inla.org>).
Imports: stats, ape, Rcpp, Matrix, methods, graphics, dplyr, lme4,
Suggests: testthat, pez, tidyr, knitr, rmarkdown, covr, picante,
rbenchmark, INLA, MCMCglmm, logistf, phylolm