Benchmark large-scale phylogenetic data sets, including supermatrix, supertree and gene-tree parsimony data sets

Data set/ taxa	Analysis	Genes/ Trees	Number of taxa	Chars/ MRP chars	Density	Published Score	Algorithm	Comments	Download**	Publication
Green Plant Protein	Cluster-taxon graph	853	14502	-----		----		Single-copy informative clusters	-Cluster-Taxon Table	Driskell et al. 2004
	Super-matrix	254	69	96698	0.16	86876	MP Heuristic search	Protein parsimony step matrix	-All 254 alignments -Supermatrix -One MP tree
	Supertree	254	69	1899	0.33	2962	MP Heuristic search on MRP matrix	One MP tree per locus used as input to MRP	-All 254 MP trees -MRP matrix -8 MRP trees	Unpublished results
Papilionoid Legumes	Cluster-taxon graph	47	2236	----	----	----		Single-copy informative clusters in “dense” analysis	-Cluster-Taxon table	McMahon and Sanderson (2006)
	Super-matrix	39	2228	33168	0.043	56093	MP Heuristic search		-All 39 alignments -Supermatrix -5000 MP trees
	Local Alignment	1	123	----	----	----	Diagonal alignment (Dialign)	Data are various sets of ITS1, 5.8S, ITS2 and flanking rDNA regions	-Fasta file of sequences -Clustalw file of alignment output
Seed Plant ESTs	Cluster-Taxon graph	577	7						-Cluster-Taxon table	Sanderson and McMahon (2007)
	Gene tree parsimony	577	7	----		796.3	Exhaustive search among 945 rooted species trees	Multiple equally parsimonious gene trees downweighted according to frequency	-All rooted gene trees (built with MP; midpoint rooted) -Optimal species tree
	Gene tree parsimony	577	7	----		779.0	Exhaustive search among 945 rooted species trees	Multiple ML gene trees downweighted according to frequency	-All rooted gene trees (built with ML; midpoint rooted) -Optimal species tree

**Note many of these files are compressed. Formats used include:

-Cluster-Taxon table: Two columns, first column is cluster ID number; second column is GenBank taxon ID number

-Supermatrix and tree files: Nexus format

-Alignments: Flat file containing multiple Nexus files