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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ggtree plotting area not big enough

I am trying to plot a circular phylogenetic tree with bootstrap labeled nodes and user defined/colored tip labels. I got the bootstrap results and labels to work properly, but somehow I just couldn't fully draw the plot in my graphic device. There…
user2927760
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change specific parts of a string in python (update bootstrap values in phylogenetic trees)

So basically I have a string: string_1 = '(((A,B)123,C)456,(D,E)789)135' Containing a phylogenetic tree with bootstrap values is parenthetical notation (not really important to the question, but in case anyone was wondering). This example tree…
Andrew WM
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Phylogenetics in R: collapsing descendant tips of an internal node

I have several thousand gene trees that I am trying to ready for analysis with codeml. The tree below is a typical example. What I want to do is automate the collapsing of tips or nodes that appear to be duplicates. For instance, descendants of node…
spiral01
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How to get the node order of phylogenetic tree in R?

I used the R package ggtree to plot a phylogenetic tree and I need to know the order of the tips so that I can combine it with specific information for each tip. Of course I can manually record the order, but I have a lot of these trees. What's…
yorven
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ETE2 - One Child Node with Multiple Parents?

I'm trying to create a tree using the ETE2 module in Python. I'd like to add 1 child node to 2 parent nodes so that they both connect to the child when the tree is displayed. I'm a complete novice with ETE, so please forgive me if this is an easy…
user2740614
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R- How to plot correct pie charts in haploNet haplotyp Networks {pegas} {ape} {adegenet}

When using the haploNet package to make some plots on a haplotype network, I used a script available on the internet to do so. However I think there is something wrong. The script is available in form of the woodmouse example. The code I used is: x…
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How to plot Pie charts in haploNet Haplotype Networks {pegas}

I'm trying to use haploNet function of {pegas} to plot a haplotype network, but i`m having trouble putting equal haplotypes from different populations in a same piechart. I can build a haplotype net with the following script: x <-…
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Missing Tree Tips When Plotting Phenogram

When I generate a phenogram using the phytools package, the tips and tip labels of the trees are not displaying. Does anyone have any ideas on how to fix this, or another way of plotting a phenogram with nodes and tips with a y axis plotted at the…
Hannah O.
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Multicoloured lines on phylogeny plot in R

In R I would like to make some graphs in which I use multicoloured lines as in the examples below. Perhaps I could do this using different lines placed next to each other, but the problem is that it is hard then to use the correct line width so that…
Tom Wenseleers
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R: newick tree from list of lists

I am working on to create a newick tree out of list of childs. I have a list of lists where the list name is the parent name and list element are the childs. Here is an example: $`825` [1] 824 $`824` [1] 823 $`823` [1] 822 $`822` [1]…
Rachit Agrawal
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R distance matrix format from already calculated data

This is my first time working with R. I have a table with 3 columns and 12090 rows (156 bacteria). The first two columns are names of bacteria and the last column is a number indicating relatedness between the organisms (based on a kind of genome…
Binnie
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Simulate stochastic bipartite network based on trait values of species - in R

I would like to create bipartite networks in R. For example, if you have a data.frame of two types of species (that can only interact across species, not within species), and each species has a trait value (e.g., size of mouth in the predator…
sckott
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How to wrap uninterrupted text in Latex?

I need to insert text like this in my Latex…
Helene
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How can I change the font family of tip labels in a phylogenetic tree in R ape package when saving to devSVG?

I have several phylogenetic trees imported into R from Newick format. I am using the ape package to plot the trees with plot.phylo command. I would like to be able to change the font family (not only the size, which I can do with cex, or color with…
antass
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Identifying list elements contained in another list that are both elements of a data frame

I have two data frames, DF1, DF2, each with two columns (a, b). One column (a) is a unique identifier the other is a column (b) with elements that contain a list. The list contains label names. I would like to search DF2$b elements to see if they…
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