[Bioperl-l] Script taxonomy2tree version 1.4 crashed on 110 species

Chris Fields 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().
>
> Gabriel

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.

chris


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