All Questions
20 questions
2
votes
1
answer
64
views
Error importing Maximum Credibility Tree from BEAST into R using treeio's read.beast()
I've encountered an issue that I'm hoping someone can help with. I constructed a phylogenetic tree using BEAST1 and then extracted the Maximum Credibility Tree using treeannotator. I'm trying to ...
1
vote
0
answers
95
views
How to identify all descendents of a branch on a phylogeny
I'm trying to simulate the evolution of binary traits on phylogenies in R to end up with a dataset of the traits held by each tip. Starting at the root, at every timestep, new traits are added with a ...
3
votes
1
answer
303
views
Plot phylogenetic tree from list of edges
I have a dataset that I wish to convert to tree or phylo format like in the ape package, in order to plot the phylogenetic tree. It is formatted like a list of ...
- 33
1
vote
1
answer
178
views
Phylogeny building in R from FASTA files:
Im working on building a phylogeny from scratch with downloaded FASTA sequences from GeneBank. I think Im doing alright up until the multi sequence alignment in the ...
- 111
3
votes
2
answers
2k
views
R ggtree apply colors to branches with multiple colors
This question was also asked on StackOverflow
I have a phylogenetic tree made with a Newick format
((a:1,b:1):2, (c:1, d:1):3):1;
The output will be
I have drawn ...
- 45
2
votes
2
answers
199
views
Create a NHX phylogeny format with r or python
I need help to add information in my phylogenetic tree on each branch.
I have two pieces of information at my disposal:
A phylogenetic tree in newick format :
(mammal:0.14,turtle:0.02,(rayfinfish:0....
- 199
2
votes
1
answer
484
views
Plot information stored in dataframe within a tree (ggtree)
Hello to the entire Stackoverflow community!
I'm writing to you because I'm currently building a phylogeny with ggtree and I have in parallel a table like this one:
df :
...
- 199
3
votes
4
answers
1k
views
Comparing phylogeny in R
So I want to compare the phylogeny created using two methods for example Maximum likelihood and maximum parsimony.Is there any way to compare the two phylogeny ?
I did read about phangorn but not ...
- 1,854
1
vote
1
answer
271
views
Phylogenetics software that can represent collapsed nodes as triangles
I am trying to represent a large (100-300+ sequences) phylogenetic tree in a way that gets my point across. I figured that reducing the number of branches (by collapsing clades which include highly ...
- 1,027
1
vote
1
answer
443
views
phangorn fasta file read error
Im trying to read a multifasta sequence file into phangorn I get the following error
...
- 1,854
2
votes
1
answer
188
views
How to interpret Mendelian randomization results?
I did Mendelian randomization using this software:
https://cran.r-project.org/web/packages/MendelianRandomization/vignettes/Vignette_MR.pdf
...
anamaria
2
votes
2
answers
447
views
Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?
I would like to visualize tree with multiple sequence alignment.
My din.newick file is shown below,
...
- 109
5
votes
2
answers
318
views
Calculate the percentage of each unique phylogenetic tree in a BEAST output
I have a nexus formatted BEAST output containing 20,000 phylogenetic trees of seven taxa. Is there any way to get the percentage of each unique phylogenetic tree contained in this output?
I already ...
- 191
3
votes
1
answer
206
views
Removing genes with less than a correlation cut-off between two matrices
I have two matrices like this:
...
user3962
3
votes
1
answer
137
views
Is there an R package that computes homoplasy excess ratios (HER)?
I want to calculate the homoplasy excess ratio for a phylogenetic tree, for example homoplasy resulting from recombination.
I am wondering if there are any R packages out there that will do this?
I ...
- 317
5
votes
2
answers
312
views
How to plot character state changes from a presence-absence matrix on to a phylogeny
I wish to assign character state changes from a presence-absence matrix to a phylogeny. Thus I want to identify the most parsimonious hypothesis for which node and branch a given "mutation" or "change"...
- 151
3
votes
2
answers
1k
views
How do I estimate branch length of a maximum parsimony phylogeny in R?
I am trying to estimate a phylogenetic tree in R with ape and phangorn. With pratchet() and optim.parsimony(), I can estimate a ...
- 317
4
votes
1
answer
224
views
Problems in creating desired phylogenetic tree with ggtree
I am working on haplotype data and want to make a tree out of haplogroups using ggtree. I have following data in newick format.
...
4
votes
2
answers
5k
views
How to convert a phylogeny to a dendrogram in R
I want to convert my phylogeny into a dendrogram so I can use it with dendextend in R to produce a tanglegram. I have made some progress but I keep encountering errors, see below:
...
- 965
10
votes
4
answers
4k
views
How do I generate a color-coded tanglegram?
I want to compare two phylogenies and colour the association lines based on some metadata I have. I have been using ape cophyloplot but I have not had any success in getting the lines to colour ...
- 965