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
what kind of format you have?
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
is this do the job?
http://pycogent.org/cookbook/building_phylogenies.html
http://etetoolkit.org/docs/latest/tutorial/index.html
http://biopython.org/wiki/Phylo
@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...