Except for the dataset at 0 min with larger average RPKM values (discussed below), all other datasets had similar distribution patterns (Additional file 8A).
It is worth noting that the topology supporting a basal position of the mouse-related clade is again the least supported, except for the dataset with maximum rate ≤ 0.5.
Except for one, the datasets in Benchmark 2 are all of very high dimension (at most 1277-see the Supplementary File).
The data were obtained as CEL files in all datasets, except for the two datasets on lung cancer grade in which the data are available only as Gene Expression Omnibus (GEO) series matrix files.
A summary of the results for Consensus with H = 250 and p = 80%, on all algorithms, except NMF, and for the datasets in Benchmark 2. The table legend is as in Table 1.
A summary of the results for FC with H = 250 and p = 80%, on all algorithms, except NMF, and for the datasets in Benchmark 2. The table legend is as in Table 1.
Except for the BRN and SRBC datasets (which are only available as preprocessed in their originating studies), datasets are preprocessed and normalized based on the recommended procedures [ 13] for Affymetrix and cDNA microarray data.
From these figures, we find that the median genomes returned by GRAPPA-TP are the closest to the true ancestors, except for the easy datasets with 100 genes and r = 4, where the DCJ median actually performs better.
Table 1 shows in detail the results obtained for the datasets tested except for the the Tree-of-Life dataset.
All datasets, partition files and starting trees, except for the unpublished dataset d37831_6, are available for download at http://wwwkramer.in.tum.de/exelixis/pointerMeshData.tar.bz2.
