Difference between revisions of "SPR Supertrees example datasets"

From Bioinformatics Software
Jump to navigationJump to search
(New page: __NOTOC__ == 244 Taxa Bacterial Supertree == A recent presentation at iEvoBio 2012 demonstrated a 244-taxa bacterial SPR Supertree constructed from a subset of the data from the 159,905 ...)
 
Line 2: Line 2:
  
 
== 244 Taxa Bacterial Supertree ==
 
== 244 Taxa Bacterial Supertree ==
 +
 +
[[Image: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 [[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.
 
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.
  
The constructed tree is available in [[media:244_taxa_supertree|newick]] and [[media:244_taxa_supertree_colored|colored nexml]] formats.
+
The constructed tree is available in [[media:244_taxa_supertree|newick]] format.

Revision as of 13:12, 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.