I want to calculate the Moran index for several random phylogenetic trees from a data set. As the result I want a list of: the values of Moran index ...
I want to calculate the Moran index for several random phylogenetic trees from a data set. As the result I want a list of: the values of Moran index ...
I have a time-calibrated phylogenetic tree from BEAST and I would like to make a figure in which its nodes are rotated to match an arbitrary ordering. ...
. Answers to this question are eligible for a +50 reputation bounty. Ge ...
I have a dataset which consists of 89 specimens, these are placed into clades as shown in the table below as an example. They also have 5 continuous v ...
I have 96 amino acid sequences which I aligned with MAFFT and trimmed manually (FASTA format), choose the model of amino acid substitution with ProtTe ...
I have a tree and I want to get part of the tree that is ancestors of cutree groups. I am using cutree to get a certain number of groups: How ...
I'm trying to place a phylogeny at the middle of a composite plot. I however fail to find the proper setting for this, as either the names on top& ...
I'm new to programming in R and trying to do a very specific task. I have a fasta sequence of n samples, which I read in ape: This created a matri ...
I am trying to create a figure of a map of a continuous trait onto a phylogenetic tree using the ape and phytools packages in R for a publication. An ...
I am trying to visualize the results of a phylogenetic least squares regression using ape and phytools. Specifically, I have been trying to create a r ...
I am trying to create a tree to calculate phylogenetic signal and conduct a phylogenetic generalized least squares analysis. However, some of my taxa ...
I just re-visited an old r script to double check my analyses. I'm getting this new error when I try to run PGLS: No covariate specified, species ...
I have a dataset with different levels of branches starting from the top level: stock -> mbranch -> sbranch -> lsbranch. I want to be able to ...
I have two trees that I am trying to compare. One from mrbayes, another from Paup. When I use read.nexus, the resulting phylo objects have differentl ...
Given a multiPhylo object in R, what's the simplest way to count the number of duplicate topologies. For instance, if I randomly sample from all 15 po ...
tree is a phylogenetic tree (proved with class(tree) ). I already tried to reinstall phyloseq but it does not help. How to avoid this error? ...
I would like to generated unrooted neighbour joining trees from input haplotype data, and then colour the branches of the trees based on a variable. I ...
I am trying to calculate phylogenetic signal using the phylosig function from phytools, but I get this error: However, when I check my tree, it sa ...
I am trying to create a character map and was recommended to use Phylotools and Ape packages in R. I have installed the packages but when I try to do ...
I'm trying to write an Rscript to run the phylogenetics package ape to run the same command on many input files and produce an output file for each on ...