I need to access global phylogenies, going down to the species level if possible. Is there a resource that provides different resolutions of the Tree of Life, based on our current knowledge about it?
Just one word of caution, NCBI taxonomy is very convenient to access, but I think they claim not to be an authoritative taxonomic source (at least this was the case previously). I took this to mean that it may not reflect latest taxonomic thinking in any particular taxonomic group.
Edit: latest from their website:
"The Entrez Taxonomy database is curated by a small group of taxonomists at the NCBI, based on the current consensus classification in the systematic literature. We try to maintain a phylogenetic classification (containing only monophyletic groups, whenever possible) but it is not automatically generated from the sequence data itself. Although there are a growing number of species with complete genomes in GenBank, the vast majority of species in Entrez Taxonomy are represented by a small snippet of sequence data, not sufficient to construct a robust phylogeny."
Do you mean that your are looking for mega-phylogenies under newick format ?
Thank you all for your answers! I settled for downloading the full NCBI Taxonomy tree via http://itol.embl.de/other_trees.shtml.
Just one word of caution, NCBI taxonomy is very convenient to access, but I think they claim not to be an authoritative taxonomic source (at least this was the case previously). I took this to mean that it may not reflect latest taxonomic thinking in any particular taxonomic group.
Edit: latest from their website:
"The Entrez Taxonomy database is curated by a small group of taxonomists at the NCBI, based on the current consensus classification in the systematic literature. We try to maintain a phylogenetic classification (containing only monophyletic groups, whenever possible) but it is not automatically generated from the sequence data itself. Although there are a growing number of species with complete genomes in GenBank, the vast majority of species in Entrez Taxonomy are represented by a small snippet of sequence data, not sufficient to construct a robust phylogeny."
You should have a look at www.onezoom.org. They are working with the tree of life people and other groups, to build a nice tree. Take the tutorial on how to browse the tree, because at first it looks sort of simplistic, but they have really built a lot of great features into it.
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