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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How to get correct order of tip labels in APE after calling ladderize function

I'm trying to order the rows of a dataframe based on the tip labels found in a phylogenetic tree. The way I was going to do this was to use the match function similar to the answer from this question, however I'm stuck cause the tip.label property…
cts
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Making simple phylogenetic dendrogram (tree) from a list of species

I want to make a simple phylogenetic tree for a marine biology course as an educative example. I have a list of species with taxonomic rank: Group <-…
Mikko
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How to get taxonomic specific ids for kingdom, phylum, class, order, family, genus and species from taxid?

I have a list of taxids that looks like this: 1204725 2162 1300163 420247 I am looking to get a file with taxonomic ids in order from the taxids above: kingdom_id phylum_id class_id order_id family_id genus_id …
aLbAc
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How display length of branches in phylogenetic tree

Here I have code that draw simple phylogenetic tree from newick format: library(ape) t<-read.tree(text="(F:4,( (D:2,E:2):1,(C:2,(B:1,A:1):1):1):1);") plot(t,use.egde.length=TRUE) i am"displaying" correct length of branches, but i want all branch…
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Newick tree representation to scipy.cluster.hierarchy linkage matrix format

I have a set of genes which have been aligned and clustered based on DNA sequences, and I have this set of genes in a Newick tree representation (https://en.wikipedia.org/wiki/Newick_format). Does anyone know how to convert this format to the…
themantalope
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In python, how can I change the font size of leaf nodes when generating phylogenetic trees using Bio.Phylo.draw()?

I am using the Phylo package from Biopython to create phylogenetic trees. For big trees, I need to decrease the fontsize of the leaf nodes. It has been suggested to change matplotlib.pyplot.rcParams['font.size'] but this only allows me to change…
madcap
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cluster presentation dendrogram alternative in r

I know dendrograms are quite popular. However if there are quite large number of observations and classes it hard to follow. However sometime I feel that there should be better way to present the same thing. I got an idea but do not know how to…
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Cladogram, tree of life, cladistics, taxonomy in JS or canvas?

Good people - I need some help to find a way to create an interactive cladogram or phylogenetic tree (yes, I have read all related posts, and do not find what I am looking for). The thing is, I need the nodes to be name-able. An example would be…
benteh
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How does bootstrapping improve the quality of a phylogenetic reconstruction?

My understanding of bootstrapping is that you Build a "tree" using some algorithm from a matrix of sequences (nucleotides, lets say). You store that tree. Perturb the matrix from 1, and rebuild the tree. My question is: what is the purpose of 3…
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Change Dendrogram leaves

I want to modify the properties of the leaves in a dendrogram produced from plot of an hclust object. Minimally, I want to change the colors, but any help you can provide will be appreciated. I did try to google the answer, but but every solution…
Btibert3
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How to collapse branches in a phylogenetic tree by the label in their nodes or leaves?

I have built a phylogenetic tree for a protein family that can be split into different groups, classifying each one by its type of receptor or type of response. The nodes in the tree are labeled as the type of receptor. In the phylogenetic tree I…
RDlady
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Dendrogram edge (branch) colors to match tip (leaf) colors (ape package)

I'm trying to add color to the edges (lines) of a phylogeny-type plot in R using the plot.phylo command from the ape package. This example is for a "fan" type plot, though I expect the approach would be the same with a "phylogram type" or…
David Roberts
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phylogenetic tree comparison

I developed new algorithm for phylogenetic tree comparison(phylogenetic tree is simply rooted binary tree). As an input we have two trees, we want to calculate their similarity percentage. one example of these type of algorithms is here. But most of…
user1164667
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R phylo object: how to connect node label and node number

A phylo object in R can have internal node labels (phylo_obj$node.label), but many R functions use node numbers instead of the node labels. Even the phylo object itself uses node numbers to describe the edges (phylo_obj$edge) and does not seem to…
sharchaea
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Usning cutree with phylo object (unrooted tree) in R

I would like to use the cutree() function to cluster a phylogenetic tree into a specified number of clades. However, the phylo object (an unrooted phylogenetic tree) is not unltrametric and thus returns an error when using as.hclust.phylo(). The…
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