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48000 simulated, 12-taxon datasets
"Quartet based phylogenetic inference: improvement and limits."
Ranwez V., Gascuel O.
Molecular Biology and Evolution. 2001 18:1103-1116.
These
datasets were used in our
MBE’01 paper to compare quartet-based and other phylogenetic methods.
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FastME datasets
"Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle."
Desper R., Gascuel O.
Journal of Computational Biology. 2002 9(5):687-705.
"Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting."
Desper R., Gascuel O.
Molecular Biology and Evolution. 2004 21(3):587-598.
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PhyML datasets
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood."
Guindon S., Gascuel O.
Systematic Biology. 2003 52(5):696-704.
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PhySIC data sets
"PhySIC server: a veto supertree method with induction and non-contradiction properties."
Ranwez V., Berry V., Criscuolo A., Fabre P.H., Guillemot S., Scornavacca C. and Douzery E.J.P.
Systematic Biology. 2007 56(5):798-817.
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Phylogenomic data sets
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PhyD* datasets.
"PhyD*: Fast NJ-like algorithms to deal with incomplete distance matrices."
Criscuolo A., Gascuel O.
Submitted.
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SDM datasets.
"SDM: a Fast Distance-based Approach for (Super)Tree Building in Phylogenomics."
Criscuolo A., Berry V., Douzery E.J.P., Gascuel O.
Systematic Biology. 2006 55(5):740-755.