[Bioperl-l] Script taxonomy2tree version 1.4 crashed on 110 species
cjfields at uiuc.edu
Mon Dec 18 23:41:16 EST 2006
On Dec 18, 2006, at 10:18 PM, Gabriel Valiente wrote:
> Thanks a lot for the prompt answer and follow-up discussion. I
> think this turned out not to be a bug in the merge_lineage() code
> but a direct consequence of building a phylogenetic tree instead of
> a taxonomic tree, aka with internal node labels.
> In order to reconstruct the NCBI taxonomy for the set of species
> present in a given phylogenetic tree, the only reasonable work-
> around seems to be a first step of merging lineages and contracting
> linear paths with the current implementation, followed by a second
> step of restricting the given phylogenetic tree to the set of
> species present in the obtained NCBI taxonomy. But this does not
> affect the code for merge_lineage().
I did notice one thing, though it's minor: if you use the option to
retrieve the data from Entrez, a few species aren't found (even
though they show up in a local taxonomy search). I think both were
E. coli strains.
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