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 describ...

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...

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 ...

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 nee...

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 fa...

I want to draw a symbol (cross) anywhere along an edge of a phylogeny with R. Let us take that tree: tree.mod (((((hg19:0.0295977,macFas5:0.0351997)hg19-macFas5:0.0796862,otoGar3:0.153768)hg19-o...

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"display...

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 questi...

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 wou...

Following a previous post (Label and color leaf dendrogram in r) I have a follow-up question. My questions are similar to the post mentioned but I wonder can it be done using ape (e.g., plot(as.ph...

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.rcPara...

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 di...

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 s...

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 <- c("Benthos","Benthos","Benthos","Benthos",...

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 ...