General phylogenetic tree package
1
0
Entering edit mode
4.8 years ago
shai2go • 0

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.

Thanks

python r phylogenetic tree • 1.6k views
ADD COMMENT
0
Entering edit mode

what kind of format you have?

ADD REPLY
0
Entering edit mode

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.

@medhat

ADD REPLY
0
Entering edit mode

@medhat

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 REPLY
1
Entering edit mode
4.8 years ago

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 COMMENT
0
Entering edit mode

@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?

thanks.

ADD REPLY

Login before adding your answer.

Traffic: 1730 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6