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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Error using treedata() from geiger package in R

I am trying to run the following lines of code: tree <- read.nexus("~/Dropbox/Billfishes/Analysis/Phylogenies/Fish_12Tax_time_calibrated.tre"); characterTable <- read.csv("~/Dropbox/Billfishes/Analysis/CodingTableThresh95.csv", row.names =…
Hannah O.
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Can't open .biom file for Phyloseq tree plotting

After trying to read a biom file: rich_dense_biom <- system.file("extdata", "D:\sample_otutable.biom", package = "phyloseq") myData <- import_biom(rich_dense_biom, treefilename, refseqfilename, parseFunction = …
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Aligning metagenomic reads (OTU representatives) to my phylogenetic tree ~AND~ evaluating how multiple samples align

So... I am working with amino acid sequences. I got a fasta file containing reference sequences and a txt file giving the categorization (domain, subdomain, nickname etc etc etc.) for each sequence. First thing, I need to construct a tree with these…
Denny Ceccon
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Printing tip labels when using the python module dendropy to calculate pairwise distances between nodes on a phylogenetic tree?

I'm trying to create an array in python that will contain all the pairwise distances between every pair of nodes on a phylogenetic tree. I'm currently using dendropy to do this. (I initially looked at biopython but couldn't find an option to do…
Ben Jeffrey
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Loop of all regressions with previous rows

I am trying to create a general linear regression model between a variable, and all variables before that, from two matrices, for every row. I have two alike matrices with 30 rows and 41 columns, that both look like this: Subject1…
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Get clades by 'comment' items stored in a list with Biopython Phylo

I have a phylogenetic tree in newick format and I would like to get all clades featuring 'comment' items stored in list l = ['X','U','B','A','V','Z']. I can use from Bio import Phylo tree.find_elements(comment='X').next() to get all clades with…
user3184877
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Adding symbols and information to Phylogenetic tree

I am drawing a phylogenetic tree, and I would like to add something like a 'dead symbol̈́̈́' (e.g a skull) in the tips of the extinct species. I would also like to add an x-axes bar with latex symbols in the branching times (e.g $\Delta t_i$ or…
Francisco
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Color the tips of a phylogenetic tree by individual's species

I'm trying to build a phylogenetic tree with bootstrapping using the methodology defined here. Plotting the name of each individual (named 1,2,3,4,... for the sake of this examples) is not informative since I have a HUGE data set. Therefore, I want…
j91
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Reorder all trees in a multiphylo object

Hi I'm trying to reorder all of the trees in a multiphylo object which should just be a form of applying a function over a list, which I have done before. However, I can't seem to get the 'reorder' command from the package APE to work with lapply…
zc1
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Phylogenetics in R: different results when working on a tree compared to reading it in

This question stems directly from a previous one I asked here: Phylogenetics in R: collapsing descendant tips of an internal…
spiral01
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Biopython bootstrapping phylogenetic trees with custom distance matrix

I am trying to create a bootstrapped phylogenetic tree but instead of using raw multiple sequence alignment data and a standard scoring system, I want to use my own custom distance matrix that I have created. I have currently looked at…
adub
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R caper package: reading in phylogeny error

I'm fairly new to R and I'm trying Phylogenetic Generalised Least Squares (PGLS) for the first time, using the addon package 'caper'. My phylogeny consists of 125 species. I'm getting an error when I read in the phylogeny that I created in Mesquite…
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R Help creating tree for MiRKAT

I am attempting to create a tree for using with the R package MiRKAT, but as the documentation is very hard to understand, I hope someone in here can help me out. My data is in the structure: Acaryochloris Achromobacter Acidiphilium…
Esben Eickhardt
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Phyloxml: find and replace in a file

I am trying to edit tip labels in a phyloxml file, so that they consist of only 4 digits. For instance, what I currently have under name in the phyloxml file are the IDs on the left. What I want are the IDs on the right: ACOM042150-PA…
spiral01
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How to simulate desired number of birth-death trees?

I wonder How can I change below code so that desired number of trees is obtained. I know that one can run simulation for certain amount of time, but I need to simulate let's say 100 trees, all with 50 extant species. So if I…
vahab
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