From caf824101e9084bb2d9a7b99a681b6053a9defbf Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 1 Sep 2025 12:10:44 +0100
Subject: [PATCH 1/2] =?UTF-8?q?Add=20=C2=A7"Working=20with=20phylogenetic?=
 =?UTF-8?q?=20data"?=
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List packages that handle phylogenetic data, incorporating suggestions from #33.

Closes #33.
---
 Phylogenetics.md | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/Phylogenetics.md b/Phylogenetics.md
index 538ecf2..c4ada2e 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 function to identify clusters and plots corresponding morphospace from thstance 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
 

From 182997e005e0b55b664fd6fd967d9c78801ea15e Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Tue, 2 Sep 2025 15:20:31 +0100
Subject: [PATCH 2/2] Correct grammar

Co-authored-by: William Gearty <willgearty@gmail.com>
---
 Phylogenetics.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Phylogenetics.md b/Phylogenetics.md
index c4ada2e..bd872cc 100644
--- a/Phylogenetics.md
+++ b/Phylogenetics.md
@@ -109,7 +109,7 @@ Packages within the task view fall within one or more of the following task cate
 - `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 function to identify clusters and plots corresponding morphospace from thstance matrices.
+- `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.