Description: Search for phylogenetic trees that are optimal using a
Contains a "shiny" user interface for interactive tree search and exploration
of results, including character visualization, rogue taxon detection,
tree space mapping, and cluster consensus trees.
Handles inapplicable data using the algorithm of Brazeau, Guillerme and
Smith (2019) <doi:10.1093/sysbio/syy083> using the "Morphy" library.
future, phangorn (>= 2.2.1), promises, protoclust, Rcpp, Rdpack
(>= 0.7), Rogue (> 1.0.0), shiny, shinyjs, stats, TreeDist (>
Suggests: knitr, rmarkdown, Quartet, testthat, vdiffr (>= 1.0.0),

Title: Phylogenetic Analysis with Morphological Data
Description: Reconstruct phylogenetic trees from discrete data.
Inapplicable character states are handled using the algorithm of Brazeau,
Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy"
library, under equal or implied step weights.
tree space mapping, and cluster consensus trees (Smith 2022a, b)
Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>,
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>
and custom optimality criteria are implemented.
Imports: ape (>= 5.6), cli (>= 3.0), cluster, fastmatch (>= 1.1.3),
Suggests: knitr, Quartet, rmarkdown, spelling, testthat, vdiffr (>=

future, promises, protoclust, Rcpp, Rdpack (>= 0.7), Rogue (>
Suggests: knitr, phangorn (>= 2.2.1), Quartet, rmarkdown, shinytest,

Title: Phylogenetic Analysis with Discrete Character Data

Package: TreeSim
Type: Package
Title: Simulating trees under the birth-death model
Version: 1.0
Date: 2010-02-17
Author: Tanja Stadler
Maintainer: Tanja Stadler <tanja.stadler@env.ethz.ch>
Depends: ape, geiger
Description: The package simulates phylogenetic trees under a
constant-rate birth-death process, conditioned on having a
fixed number of final tips, or a fixed age, or a fixed age and
number of tips. When conditioning on the number of final tips,
the method allows for shifts in rates and mass extinction
events during the birth-death process. TreeSim further samples
appropriately trees with n final tips from a set of trees
generated by the common sampling algorithm stopping when a
fixed number m>>n of leaves is first reached. This latter
method is appropriate for m-tip trees generated under a big
class of models (details in the bd.gsa.taxa man page).
License: GPL-2
LazyLoad: yes
Packaged: 2010-02-23 16:05:33 UTC; tanja
Repository: CRAN
Date/Publication: 2010-02-23 16:18:22