Difference between revisions of "SPR Supertrees example datasets"

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(244 Taxa Bacterial Supertree)
 
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[[Image:244_taxa_supertree.png|thumb|457x540px]]
 
[[Image:244_taxa_supertree.png|thumb|457x540px]]
A recent presentation at iEvoBio 2012 demonstrated a 244-taxa bacterial SPR Supertree constructed from a subset of the data from the 159,905 prokaryotic phylogenetic trees from “Telling the Whole Story in a 10,000-Genome World” (PMID:21714939). The full trees are available at Dryad (doi:10.5061/dryad.gf39c8dc). To reconstruct this subset from the full dataset, you can use the -include_only option of spr_supertree with [[media:244_taxa_chosen|this text file of the chosen taxa]] and the parameters -allow_multi -support 0.8 -simple_unrooted. With the -valid_trees option, this will print out the trees and quit.
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A recent presentation at iEvoBio 2012 demonstrated a 244-taxa bacterial SPR Supertree constructed from a subset of the data from the 159,905 prokaryotic phylogenetic trees from “Telling the Whole Story in a 10,000-Genome World” ([http://www.ncbi.nlm.nih.gov/pubmed/21714939 PMID:21714939]). The full trees are available at Dryad ([http://dx.doi.org/10.5061/dryad.gf39c8dc doi:10.5061/dryad.gf39c8dc]). To reconstruct this subset from the full dataset, you can use the -include_only option of spr_supertree with [[media:244_taxa_chosen|this text file of the chosen taxa]] and the parameters -allow_multi -support 0.8 -simple_unrooted. With the -valid_trees option, this will print out the trees and quit.
  
 
The constructed tree is available in [[media:244_taxa_supertree|newick]] format.
 
The constructed tree is available in [[media:244_taxa_supertree|newick]] format.

Latest revision as of 13:23, 9 July 2012


244 Taxa Bacterial Supertree

244 taxa supertree.png

A recent presentation at iEvoBio 2012 demonstrated a 244-taxa bacterial SPR Supertree constructed from a subset of the data from the 159,905 prokaryotic phylogenetic trees from “Telling the Whole Story in a 10,000-Genome World” (PMID:21714939). The full trees are available at Dryad (doi:10.5061/dryad.gf39c8dc). To reconstruct this subset from the full dataset, you can use the -include_only option of spr_supertree with this text file of the chosen taxa and the parameters -allow_multi -support 0.8 -simple_unrooted. With the -valid_trees option, this will print out the trees and quit.

The constructed tree is available in newick format.