Methodology article
A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study
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* Corresponding authors: Chenhong Li cli@unlserve.unl.edu - Guoqing Lu glu3@mail.unomaha.edu
1 School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
2 Department of Mathematics, University of Nebraska, Omaha, NE 68182, USA
3 Department of Biology, University of Nebraska, Omaha, NE 68182, USA
BMC Evolutionary Biology 2007, 7:44 doi:10.1186/1471-2148-7-44
Published: 20 March 2007Additional files
Additional 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
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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
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