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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Transform data frame/matrix to a different organized matrix

I have a very similar doubt to my last one (Transform data frame into matrix with counts). Again, I have data files structured like this: OTU1 PIA0 1120 OTU2 PIA1 2 OTU2 PIA3 6 OTU2 PIA4 10 OTU2 PIA5 1078 OTU2 PIN1 …
Ma_fermar
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Compute distance matrix with values between 0 and 1 from absolute branch lengths phylogeny

I have a phylogenetic tree with absolute branch lengths in million years. How can i compute a distance matrix with values between 0 and 1?
eugenego
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Dendropy leaf_iter() error with lambda function

I'm doing some phylogenetics in Dendropy: I'm trying, following the tutorial, to traverse all the leaves of a tree using a filter (a lambda function). Using the lambda function gives an error if the iterator is leaf_iter, but not if the iterator is…
gvdr
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bioperl remove a node from newick tree

I'm trying to remove a node from a newick tree using bioperl. The tree file contains this data : (((A:5,B:5)90:2,C:4)25:3,D:10); Below is the code: use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; use strict; use warnings; my $input = new…
AWRAM
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Parsing an XML tree with RapidXML and discarding unwanted nodes

I am interested in using RapidXML to parse an XML tree; however, this XML has several layer of rows that I do not need. This is because it is a representation of a genetic tree and many layers are called "clade" which is essentially useless info to…
Jon Claus
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How to display an phylogenetic tree structure in WPF

I am a newbie to WPF. The question is about displaying a tree structure in WPF. I have a WPF app, which will connect to a remote database. One table (Taxonomy table) in the DB has two columns: "Parent node" (varchar(50)), and "Child…
Mavershang
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Phylogenetic Tree Contruction From Triplets

I've been given the task of writing a short program to create a phylogenetic tree (all data in the leaf nodes) given a data set of triplets, of the form (b, c, a), where a is the least common ancestor of b and c. I have a copy of Aho, Sagiv,…
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Ape:: consensus tree and edge length lost , are there solutions for this?

I am Abraham. Please! Somebody can help me with the problem with ape:: consensus and the branch length lost? I am having this problem too. Regards
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How to rescale trees to extreme shapes?

I'm posting this again althought @jeremycg helped me to develop the following code. It works but it does perform not what I wanted to! A quick reminder: I've got a set of trees, that I need to be measured in terms of a factor called gamma and if…
Jack
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R: Multiple Regression Error (Missing true/false where needed)

My R sessionInfo() of the failed runs: R version 3.1.2 (2014-10-31) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United…
user3834916
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Bootstrap a square matrix with Matlab

I want to understand how to bootstrap a square matrix with matlab. Any suggestions?
Bioing
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How to extract a tree from R memory?

I created a phylogenetic tree using "sim.bd.taxa.age". I just wanted to know how can I export the tree in newick format, given that currently it's not a phylo object! library(TreeSim) Tree <- sim.bd.taxa.age(n=300, numbsim=1, lambda=2, mu=0.5, frac…
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