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.

387 questions
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Compare list of complex structures

I have two lists of complex structures (each list is a multiPhylo object containing phylogenetic trees), and I would like to find out how many times each element of the first one appears in the second one. Pretty straightforward, but for some…
jvddorpe
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Random ultrametric trees

I've implemented a program on python which generates random binary trees. So now I'd like to assign to each internal node of the tree a distance to make it ultrametric. Then, the distance between the root and any leaves must be the same. If a node…
user10795185
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Assign tree tip labels from csv file with R

I am trying to create a phylogenetic tree and for that I have aligned sequences (135 sequences) using MUSCLE and converted them to dnaBIN objects. I have also created a separate file for species name that I need to use as the tree tip labels since…
temsandroses
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conversion newick to graphml using python

I would like to convert a tree from newick to a format like graphml, that I can open with cytoscape. So, I have a file "small.newick" that contain: ((raccoon:1,bear:6):0.8,((sea_lion:11.9, seal:12):7,((monkey:100,cat:47):20,…
Gildas
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How do I annotate a ggtree object with bootstrap values?

I have a phylogenetic tree of the class phylo with 24 tips and 23 internal nodes. I ran a bootstrap analysis on this tree and the data using boot.phylo, which returned a vector of 23 bootstrap values. I created a ggtree object from my original tree…
Namenlos
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How to plot character state changes from a presence-absence matrix on to a phylogeny

I am trying to assign character state changes from a presence-absence matrix to a phylogeny. I have tried assigning each character to its leaf node, and then if the leaf node's sister has the same character I reassign the character to the parent…
Gloom
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How does TnT (Goloboff et al., 2008) assign internal node labels?

I have used TnT v1.1 (Goloboff et al., 2008) to assign synapomorphies from a presence-absence matrix (PAM) to a phylogeny. TnT does not allow for internal node IDs or branch lengths and I need to use the branch lengths with the TnT data for…
Gloom
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Using PhyML within BioPython Phylo

I recently tried to use Maximum Likelihood for the creation of trees from an alignement file but had problems when following the official BioPython's Documentation: cmd = PhymlCommandline(input='data/random.phy') out_log, err_log = cmd() I replaced…
Nicolas
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Duplicate tips label removal: importing phylogenetic tree in R for comparison

Problem: I'm trying to import a newick format phylogenetic tree, I've done this before, (a tree made in the same way, so the code works!) however the tree appears to be the problem. I'm getting a duplicate tip labels error. If that is the case, is…
Biomage
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'use.edge.length = FALSE' doesn't seem to work when using plotBranchbyTrait() in phytools

I'm trying to create a phylogeny where the branch lengths that I've coded are represented by colour rather than length. So I want the branch lengths to be equal. Here is my code: plotBranchbyTrait(tree.scaled, tree.scaled$edge.length,…
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How can analyse a trait where I have data for multiple individuals at each tip of my phylogenetic tree?

I'm new to phylogenetic analyses, and I'm using the ape library to analyse neuroanatomical traits of 34 primates from 28 different species. I used 10ktrees to obtain a consensus phylogenetic tree (with 28 tips). However, I can't combine the…
roberto
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binary response variable and categorical predictors in phylolm package

I am using phylolm package to run a model with binary response variable (0/1), and a continuous predictor and a categorical predictor having more than 3 levels. If I consider the categorical predictor as continuous, i.e., 0, 1, 2, 3, the model ran…
phil
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Phylogenetic correlation test

I need to perform a correlation test (returning r, t and p.value) between two variables that accounts for a phylogenetic correlation structure between individuals. Is there any simple way to do that in R?
jsegrestin
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the number of rows in the data does not match the number of tips in the tree in phyloglm

I do not seem to able to see where I am getting things wrong. I am using the package phylolm to do some regressions with phylogenetic data my model is not running and returns the error : Error in phyloglm(testVar ~ ...the number of rows in the data…
Taw
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plot phylogenetic logistic regression with binary response variable

I used the phylolm package to do phylogenetic comparative analysis. As my response variable is binary data (ones and zeros), I used phylogenetic logistic regression. How do I plot the output of phyloglm? I found a similar question here, but I can't…
phil
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