I am trying to familiarize with Biopython for phylogenetics with the official documentation. https://biopython-tutorial.readthedocs.io/en/latest/noteb ...
I am trying to familiarize with Biopython for phylogenetics with the official documentation. https://biopython-tutorial.readthedocs.io/en/latest/noteb ...
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 custom tree of extinct taxa in the form of an newick file. I want to use R to create a figure of said tree with the each node having the matc ...
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. ...
I am trying to plot a phylogenetic tree using R, however I'm getting the check the edge matrix error. How can I get around this problem? I tried to ch ...
I have two data frames, DF1, DF2, each with two columns (a, b). One column (a) is a unique identifier the other is a column (b) with elements that con ...
I wanted to create a phylogenetic tree where I can trace a certain dimension throughout clades. I followed the tutorial by Winternitz 2016, but now I ...
I have a phylogenetic tree made with a Newick format The output will be I have drawn this with http://etetoolkit.org/treeview/, but output with ...
I have a phylogenetic tree with many tips and internal nodes. I have a list of node ids from the tree. These are part of a separate table. I want to a ...
I am using the phylolm function (in package phylolm) to conduct PGLS phylogenetic analysis and am having some trouble interpreting the model output. ...
I am using R "phytools" library for the 3D phylogenetic tree. And I have made 3D tree successfully with the script below The output is What I w ...
I am trying to to include my results of ancestral state estimation as pie charts at the nodes of a phylogenetic tree. It works fine for rectangular tr ...
I thought that BEAST does not allow negative lengths of branches on prior distribution level so I got very surprised when I have looked at my consensu ...
I am trying to install OpenCL for BEAGLE. First, I have downloaded intel_sdk_for_opencl_applications_2020.3.494.tar.gz from here. Then I unzipped it & ...
I'm trying to read a Newick-format tree into R. My tree file looks like this: When I read this into R with ape::read.tree(), it appears to correctl ...
I am VERY new to R, so I am sorry if this question is obvious. I would like to add multiple labels to branches in a phylogenetic tree, but I can only ...
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I am looking to rename 1290 tip labels in my phylo tree using a second df. I am able to rename one label at a time using the below code: but this i ...
I am having a hard time understanding why my phylo tree (imported as a phyloseq object from QIIME2) appears to have no branch lengths when used in phy ...
I'm using the phenogram() function in the R package phytools to plot a phylogeny along axes of relative time (x) and phenotype, in this case mean annu ...