Question: General phylogenetic tree package
gravatar for shai2go
23 months ago by
shai2go0 wrote:

I am looking for a package that will allow me to use phylogenetic tree creation algorithms, with more general data than fasta format for genetic data.

I found lots of packages but they require .fasta format and work for amino acids or nucleotides.

I need to be able to define the traits of the data, and the way of distance calculation.

I prefer something that will work in python and if not python or r.


R tree python phylogenetic • 576 views
ADD COMMENTlink modified 23 months ago by Jean-Karim Heriche16k • written 23 months ago by shai2go0

what kind of format you have?

ADD REPLYlink modified 23 months ago • written 23 months ago by Medhat7.6k

i am trying to construct phylogenetic tree for texts, so the format is somewhat more complex, a matrix of n*m, every matrix(i,j) is a word. i have a component that will calculate the distance beetween different entries of the matrix.

i can reduce the words to vector of values and can calculate distance beetween them. i need to be able to activate the phylogenetic algorithm with my own distance calculation.


ADD REPLYlink written 23 months ago by shai2go0

is this do the job?

ADD REPLYlink written 23 months ago by Medhat7.6k


all the above are good for 1.inferring trees for genetic information 2.plotting trees that are allready made.

i need to infer trees for data, that is not genetic, hence, i need to be able to create the distance matrix for it. i can't find any way to do so with what you posted...

ADD REPLYlink written 23 months ago by shai2go0
gravatar for Jean-Karim Heriche
23 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche16k wrote:

It seems you're looking to draw a phylogenetic tree using an arbitrary distance matrix as input. A number of phylogeny software can do this but they normally use generic hierarchical clustering algorithms such as implemented in the agnes() function of the R package cluster. If you really want to use a phylogeny software, you can try the R packages ape or phangorn. They have various neighbour-joining functions taking a distance matrix as input.

ADD COMMENTlink written 23 months ago by Jean-Karim Heriche16k

@Jean-karim - thanks! ape is what i wanted, nj and mvr do the trick, but a little issue, i need to construct a tree assuming that let's say, if i get 1,2,3 there is a possibility of 1 being the father of 2,3 (that are brothers). nj and mvr give me a tree where all the samples are leaves, and none of them are the father of one another,

is there a way not to assume that?


ADD REPLYlink written 22 months ago by shai2go0
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