Category "phylogeny"

What can be the reason of getting negative branches lengths after treeannotator analysis?

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 consensus tree in

Python make newick format using dataframe with 0s and 1s

I have a dataframe like this a b c d e f g h i j k l m mut1 0 0 0 0 0 1 1 1 1 1 1 1 1 mut2 0 0 0 0 0 1 1 1 1 1 0 0 0 mut3 0 0 0 0 0 1 1 0 0 0 0 0 0

Missing ',' in line when Biopython reads a nexus tree

I want to edit a tree that I got from BEAST2 treeannotator in nexus-format. Usually I use the module Phylo from Biopython for such work but Phylo.read(r"filenam

R: Building phylogenetic tree from arbitrary features?

StackExchange. I'm trying to build a phylogenetic tree for >100 individuals, using R. However, while tutorials for packages like APE and ggtree readily show

R phylo object: how to connect node label and node number

A phylo object in R can have internal node labels (phylo_obj$node.label), but many R functions use node numbers instead of the node labels. Even the phylo objec

Is it possible to use geom_insert() in ggtree for circular trees?

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 trees but I