diff --git a/Phylogenetics.md b/Phylogenetics.md index 538ecf2..bd872cc 100644 --- a/Phylogenetics.md +++ b/Phylogenetics.md @@ -104,6 +104,15 @@ Packages within the task view fall within one or more of the following task cate - `r github("Leonardini/treeCentrality")` can compute several statistics inspired from network science. +## Working with phylogenetic data in R + +- `r pkg("phangorn")`, `r pkg("TreeTools")` and `r pkg("TreeSearch")` contain functions for reading phylogenetic datasets into R and manipulating the resulting objects. +- `r github("uyedaj/rphenoscate")` allows character matrices to be synthesized from semantic phenotype data, and facilitates analysis of "inapplicable" characters – such as morphological characters that are dependent on a parent trait – by constructing formal character hierarchies and the corresponding rate matrices (Tarasov 2023). +- `r pkg("phenex")` facilitates the annotation of character matrices files with ontology terminology. +- `r pkg("Claddis")` and `r pkg("EvoPhylo")` generate distance matrices from phylogenetic data, with functions to identify clusters and plot the corresponding morphospaces from these matrices. +- `r pkg("geiger")` and `r pkg("phangorn")` contain functions to simulate phylogenetic data from phylogenetic trees. + + ## Tree building in R ### Phylogenetic inference @@ -115,7 +124,6 @@ Packages within the task view fall within one or more of the following task cate - `r github("helixcn/phylotools")` can build supermatrices for analyses in other software. - `r pkg("EvoPhylo")` can be used to perform automated morphological character partitioning for bayesian phylogenetic analyses that are performed with [MrBayes](http://nbisweden.github.io/MrBayes/) and [BEAST2](https://www.beast2.org/). It can also be used to analyze the macroevolutionary parameter outputs from such analyses. - `r bioc("fastreeR")` can be used to calculate distances, build phylogenetic trees, or perform hierarchical clustering between the samples of a VCF or FASTA file. -- `r github("uyedaj/rphenoscate")` facilitates analysis of "inapplicable" characters – such as morphological characters that are dependent on a parent trait – by constructing formal character hierarchies and the corresponding rate matrices (Tarasov 2023). ### Divergence times