Is there any function available in Phylo.jl to read phylogenetic trees from xml file?

EcoJulia / Phylo.jl

Simple phylogenetic trees in Julia to work with Diversity.jl - https://github.com/EcoJulia/Diversity.jl

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Is there any function available in Phylo.jl to read phylogenetic trees from xml file? #62

Open efmanu opened 3 years ago

efmanu commented 3 years ago

Hi, I am looking for a function to read phylogenetic trees from xml file, something similar to following python implementation:

from Bio import Phylo
# download this from http://www.phyloxml.org/examples/apaf.xml
tree = Phylo.read('apaf.xml', 'phyloxml')

Can anyone reply?

mkborregaard commented 3 years ago

There isn't anything in Phylo for this right now.

richardreeve commented 3 years ago

Does anyone actually use phyloxml? I've actually never heard of it before and a lot of the links from the phyloxml website seem broken... if it's a common format we could look into supporting it, but it doesn't seem very popular - for instance google returns ~60M hits for nexus format and ~350k for newick format (both of which Phylo supports), but only ~16k for phyloxml format.