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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Alter a file using information from another file

I want to alter the names in a phylip file using information from another file. The phylip is just one continuous string of information, and the names I want to alter (e.g. aaaaaaabyd) are embedded in it. Like…
user3767953
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Error while using ace function of ape package

I am trying to reconstruct ancestral state of continuous characters. When I use the Ace function of ape package, there is an error message which reads : Error in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) : …
user6385
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Puzzling average of correlated measurements

I submitted this question to stat.stackexchange https://stats.stackexchange.com/questions/147909/puzzling-average-of-correlated-measurements but it looks like it fits more into that forum, as it may be more a computing issue than a statistic one: I…
Xavier Prudent
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especify width to concrete branches in a plot.phylo

I want to mark different branches on a phylogenetic tree using 3 different line widths. How can I especify that branch 2 has width= 2, line 10 has width= 4 and the remaining lines have width=1? For example, there are 88 branches in the bird.orders…
Santi XGR
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Heatmap with categorical variables and with phylogenetic tree in R

:) I have a question and did not find any answer by personal search. I would like to make a heatmap with categorical variables (a bit like this one: heatmap-like plot, but for categorical variables ), and I would like to add on the left side a…
tlorin
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Terminals being renamed None with Biopython Phylo

I have been using Biopython to align some amino acid sequences with Clustal-Omega, then import the tree generated. from Bio.Align.Applications import ClustalOmegaCommandline from Bio import AlignIO from Bio import Phylo clustalomega_cline =…
jargogler
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How to get studentized residuals from pgls() in Caper R package

I have a dataset with 135 species, 6 life history traits (response) and 2 environmental variables(predictor). I am interested in doing a pgls regression analysis using the package Caper to look at the influence of the environmental variables on each…
PBA
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Link tip labels to phylogenetic tree using dots and fix overcrowded tip labels

I'm attempting to produce an ancestral reconstruction using the ape and phytools package in Rstudio. My problem is that in my phylogenetic tree the tip labels / species names are overcrowded and illegible. Currently, my tree has a dataset of 262…
notesosa
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Adding new nodes to a Tree by dendroPy

I would like to create a tree by dynamically adding nodes to an already existing tree in DendroPy. So here is how I am proceeding, >>> t1 = dendropy.Tree(stream=StringIO("(8,3)"),schema="newick") Now That creates a small tree with two children…
Hirak Sarkar
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Can I use genetic distances in form of a .csv file to create a tree in R using ape ?

It is my first time using R for phylogenetics work and I was wondering if I could do that. It seems a rather trivial job and I think there must be a very small code for this, but I am unable to get it done. Any help appreciated!
Anurag Mishra
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Difference running Rscript vs source with ape library

I have the following script in a file (call it "temp.R"): library(ape) tree <- rbdtree(0.5, 0.05, 5) bd.time(tree, 0, 0) When I run Rscript temp.R I get some results: $par birth death 0.5289875 0.0000000 $SS [1] 9.21573 $convergence [1]…
redcurry
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Phylogenetic tree

I am working to have a phylogenetic tree based on pairwise-data of genes.Below is my subset of the data(test.txt).The tree does not has to be constructed on the basis of any DNA sequences,but just treating it as words. ID gene1 gene2 1 ADRA1D …
Rgeek
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Understanding Small Parsimony, Sankoff's Algorithm

Small Parsimony Problem: Find the most parsimonious labeling of the internal vertices in an evolutionary tree. Input: Tree T with each leaf labeled by an m-character string. Output: Labeling of internal vertices of the tree T minimizing the…
user2808302
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Phylocom non-ultrametric tree vs ultrametric tree

Again. I need help one more time. Nowadays I am getting into PHYLOCOM software for inferring characteristics of a phylogeny from different samples. This software allows you to calculate if your species are showing clustering or overdispersion within…
Ma_fermar
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Branch length modification of a phylogenetic tree in R

I have a phylo file in NEWICK format with a few distance of a very little length (aprox. of 1.042e-06) and I need to "eliminate" these little distances. I have thought to multiply all distances by 10, because for what I further need the tree this…
Ma_fermar
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