Questions tagged [phylogeny]

Phylogeny is the study of relationships between items (organisms, concepts, etc); typically represented by phylogenetic trees. Such trees may simply reflect evolutionary relationships; or their branches may be scaled according to some measure of evolutionary distance, such as accumulated mutations or time.

Phylogeny is the study of relationships between items (organisms, concepts, etc). The primary use of phylogeny is in systematics, the inference of evolutionary history from morphological and/or molecular data; this typically requires computational methods. Relationships are often depicted as trees, whose branches may scale according to an aspect of evolutionary distance, such as number of mutations, or time. When temporal and/or geographic data are available, phylodynamic or phylogeographic analyses can be performed.

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How do I fix a "badly conformed" phylogenetic tree in order to plot it in R?

I am trying to plot a tree of an inferred eucalypt phylogeny in R using the package ape. The tree is from a nexus file (Eucalypt_Bayes_dated_character_mapped.nex) that I downloaded from CSIRO's website…
cflax
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Cannot import name 'TextFace' error while using ETE3 for Phylogeny Tree

I am trying to install ETE3 for phylogeny analysis but while installing it is showing error:cannot import name 'TextFace' I tried all the available options but could not succeed. Any help will be appreciated. PS: I am trying to build Phylogeny tree…
shivam
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Phylo correlogram in R bootstrapping error?

I am trying to create a phylo correlogram based on my data using phyloCorrelogram from the phylosignal package in order to test for presence of a phylogenetic signal. My data is in the so-called phylo4d format and is called tree. Now, when I run…
Geomicro
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phylogeography: how to combine phylogenetic tree and geographic map, and create segments between tips and sampling localities with gg* packages?

I am trying to do something similar to what is described in the blog here but using R with ggtree, ggmap, and ggplot2. I want to be able to combine the plots of the phylogenetic tree and the map showing the sampling locations of the tips on a…
Eve
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Complex eigenvalues in Principal Coordinate Analysis (PCoA)

I'm sharing a problem related to complex eigenvalues in Principal Coordinate Analysis (PCoA). Any help much appreciated! The aim: perform PCoA on a matrix of phylogenetic distances -> include the ordination axes in a regression model to account for…
M. Riera
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Cannot install 'shiny' either 'bslib' package

I am trying to install the package 'phylosignal' and I have some errors related to the installation of 'shiny' and 'bslib' packages. I have tried several solutions I found but none of them have worked properly. I have updated all my packages but,…
JMTorres
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Mixed data partitions in phylogeny reconstruction in R

Let's have two matrices, one DNA sequence alignment and one consisting of binary characters. dna <- matrix(c("a", "a", "a", "t", "a", "a", "t", "t", "a", "g", "c", "c"), ncol = 4, dimnames = list(LETTERS[1:3],…
nya
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Select all samples with a specified base at a particular position

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: library(ape) matrix <- read.dna(myfasta, format="fasta", as.character=TRUE) This created a matrix, like so: | | V1 |…
granny
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Is there a way to manually adjust the boundaries of a color gradient on a phylogeny in ape/phytools?

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 regression equation for predictive purposes, and I am looking at how much phylogenetic signal…
user2352714
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I have error message trying to show a phylogenetic tree using R studio, I can not upload it

I am trying to upload a phylogenetic tree named Symonds.tre that is in my working directory and is .tre library(ape) symondsTree <- read.tree("symonds.tre") Error message is: Error in if (all(phy$node.label == "")) phy$node.label <- NULL :missing…
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How to colour the branches of an unrooted tree using a variable in R

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 am using the packages Ape and ggtree. The haplotypes and co-variables (metadata) are on two…
Will Hamilton
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How does one modify the axes in MATLAB's phylogenetic tree tool?

I want to display pretty dendrograms for some agglomerative clusters I am generating in Java. I write the clusters out to a file in Newick format. Then, I can get a pretty picture that is almost what I want. tr =…
kc2001
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How do I input multiple phylogenetic trees into R?

I have 10,000 trees, as individual .tre files, in my working directory, but I can't seem to load them all into R. I tried this: library(ape) temp=list.files(pattern="*.tre") mamtrees=lapply(temp,read.tree) Which yielded the following error…
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Convert phylogenetic tree into dataframe

I am looking for a way in R to convert a phylogenetic tree (Newick format or class "phylo") into a dataframe. The goal is to get a nice overview of which tips descent from every node of the tree. Does anyone have experience with this problem? I can…
kara
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Count number of groups (with specific TAG) within a specific format (with Python)

Hello everyone I need some help : I do not know if you are familiar with phylogenetic tree but here is an exemple: /-YP_001604167.1 | |--YP_001604351.1 --| | /-seq_TAG2_Canis_taurus | /-| | | \-seq_TAG2_Canis_austracus \-| …
chippycentra
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