  Methodology articleDetecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metricsJ Gregory Caporaso1 1Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, USA 2Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands 3Computational Genomics Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia 4Center for Computational Pharmacology, University of Colorado Denver, Aurora, CO, USA 5Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
BMC Evolutionary Biology 2008, 8:327doi:10.1186/1471-2148-8-327
Additional filesAdditional file 1: Additional Table 1. Precision, recall, F-measure, total hits, and AUC data for each method, alphabet pair at different significance thresholds. This zip file contains a csv file containing all data, and a text file containing a description of the data. Format: ZIP Size: 100KB Download file Additional file 2: Additional Table 2. Top five amino acid alphabets for each method on myoglobin and myosin rod alignments. Format: PDF Size: 27KB Download file This file can be viewed with: Adobe Acrobat Reader Additional file 3: Additional Table 3. The effect of increased false positive rate on t-test p-values. Format: PDF Size: 38KB Download file This file can be viewed with: Adobe Acrobat Reader Additional file 4: Alignments and trees. The alignments and trees used in the comparisons, in fasta and newick formats, respectively. Format: ZIP Size: 38KB Download file Additional file 5: Data recreation. Documentation, scripts, and supporting data to recreate raw coevolution data. Format: ZIP Size: 18KB Download file |
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