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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Set G in prior using MCMCglmm, with categorical response and phylogeny

I am new to the MCMCglmm package in R, and rather new to glm models in general. I have a dataset of species traits and whether or not they have been introduced outside of their native range. I would like to test whether being introduced (as a binary…
Mila
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Plot phylogenetic trees face to face with links in R

I would like to plot two phylogenies opposite each other in R using the ape package. One tree has 40 nodes and one has 26 nodes: library(ape) tree1 <- rtree(40) tree2 <- rtree(26) The cophyloplot function plots these face to face with specified…
user2861089
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Use Python to extract Branch Lengths from Newick Format

I have a list in python consisting of one item which is a tree written in Newick Format, as…
PaulBarr
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Constructing a phylogentic tree

I have a list of list of lists like this matches = [[['rootrank', 'Root'], ['domain', 'Bacteria'], ['phylum', 'Firmicutes'], ['class', 'Clostridia'], ['order', 'Clostridiales'], ['family', 'Lachnospiraceae'], ['genus', 'Lachnospira']], …
BioGeek
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Normalizing a Phylogenetic Tree in R

When working with phylogenetic tree data in R (specifically when working with "phylo" or "phylo4" objects) it would be useful to normalize branch lengths so that certain taxa (the ones that evolve faster) do not contribute a disproportionate amount…
Krisrs1128
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Phylogenetic model using multiple entries for each species

I am relatively new to phylogenetic regression models. In the past I used PGLS when I had only 1 entry for each species in my tree. Now I have a dataset with thousands of records for a total of 9 species and I would like to run a phylogenetic model.…
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Italics and regular text in phylogeny tip labels in R

The following code will plot a phylogenetic tree with tip labels in italics and underscores replaced with spaces. library(ape) tr <- rtree(5, tip.label=c("a_b_x1", "b_c_2", "c_d_3y", "d_e_4", "e_f_5")) plot(tr) How can I combine regular text with…
nya
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Node labels on circular phylogenetic tree

I am trying to create circular phylogenetic tree. I have this part of code: fit<- hclust(dist(Data[,-4]), method = "complete", members = NULL) nclus=…
Vis
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Combine phylogenetic tree with x,y graph

I'm trying to arrange a phylogenetic tree onto a graph showing physiological data for a set of related organisms. Something like the picture below. This was put together in powerpoint from 2 separate graphs. I guess it gets the job done, but I…
user2055130
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Check if two trees are equivalent

The following are three equivalent representations of the same tree (phylogenetic). I am trying to figure out an algorithm to check if two tree representations are equivalent. Trees are defined to be equivalent if the parent-child relationship…
Sunder
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Change which axis is used as radial/angular position with matplotlib polar=True (Creating circular phylogenetic tree with Bio.Phylo)

If I create a phylogenetic tree using Biopython Phylo module, it is oriented from left to right, e.g.: import matplotlib.pyplot as plt from Bio import Phylo from io import StringIO handle = StringIO("(((A,B),(C,D)),(E,F,G));") tree =…
Roger Vadim
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Using a function on a column from tree file class Phylo

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 add a new column to the table, children. To get the descendants (nodes and tips), I am using…
aholtz
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Add a fossil tip to a tree

I am having a hard time trying to add several fossil tips to a 100 phylogenetic time trees. Here is a drawing of what I want to do: I would like to do it for my 100 trees contained in a single nexus file. Thank you in advance. EDIT: Okay, I figured…
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Calculate sum of the total phylogenetic branch length from species birth-death table

BACKGROUND This question is a bit complex so I will first introduce the background. To generate an example of species birth-death table (the L table) I would suggest to use dd_sim() function from DDD…
Tianjian Qin
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Adding labels to heatmaps in ete3

I read the whole documentation on profile face heatmap generation but I could not find any way to add labels to the heatmap produced by ete3. For example in the following code, the 7 columns of the heatmap have names 'Marker1' to 'Marker7'. Is there…
Masih
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