  Methodology articleA practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case studyChenhong Li1 1School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA 2Department of Mathematics, University of Nebraska, Omaha, NE 68182, USA 3Department of Biology, University of Nebraska, Omaha, NE 68182, USA
BMC Evolutionary Biology 2007, 7:44doi:10.1186/1471-2148-7-44
Additional filesAdditional file 1: Exon ID, exon length, GC content of predicted single nuclear gene markers in zebrafish and torafugu, as well the blast result between orthologous genes. Format: RTF Size: 249KB Download file Additional file 2: Results of PCR amplification of 10 new makers in 36 species of ray-finned fishes. Format: RTF Size: 165KB Download file Additional file 3: Maximum likelihood phylogeny based on protein sequences of individual genes, zic1, myh6, RYR3, Ptr, tbr1, ENC1, Gylt, SH3PX3, plagl2, and sreb2. Bootstrap value higher than 50% were mapped on branches. Format: PDF Size: 7KB Download file This file can be viewed with: Adobe Acrobat Reader Additional file 4: ML phylogenies based on protein sequences of individual genes and their out-paralogs found by relaxing our search criteria to include fragments with similarity < 50%. Format: PDF Size: 9KB Download file This file can be viewed with: Adobe Acrobat Reader |
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