Bioinformatics for DNA Sequence Analysis

1. Similarity Searching Using BLAST Kit J. Menlove, Mark Clement, and Keith A. Crandall 2. Gene Orthology Assessment with OrthologID Mary Egan, Ernest K. Lee, Joanna C. Chiu, Gloria Coruzzi, and Rob DeSalle 3. Multiple Alignment of DNA Sequences with MAFFT Kazutaka Katoh, George Asimenos, and Hiroyuki Toh 4. SeqVis: A Tool for Detecting Compositional Heterogeneity among Aligned Nucleotide Sequences Lars Sommer Jermiin, Joshua Wing Kei Ho, Kwok-Wai Lau, and Vivek Jayaswal 5. Selection of Models of DNA Evolution with jModelTest David Posada 6. Estimating Maximum Likelihood Phylogenies with PhyML Stéphane Guindon, Frédéric Delsuc, Jean-François Dufayard, and Olivier Gascuel 7. Trees from Trees: Construction of Phylogenetic Supertrees Using Clann Christopher J. Creevey and James O. McInerney 8. Detecting Signatures of Selection from DNA Sequences Using Datamonkey Art F.Y. Poon, Simon D.W. Frost, and Sergei L. Kosakovsky Pond 9. Recombination Detection and Analysis Using RDP3 Darren P. Martin 10. CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition Jesse Zaneveld, Micah Hamady, Noboru Sueoka, and Rob Knight 11. Genetic Code Prediction for Metazoan Mitochondria with GenDecoder Federico Abascal, Rafael Zardoya, and David Posada 12. Computational Gene Annotation in New Genome Assemblies Using GeneID Enrique Blanco and Josep F. Abril 13. Promoter Analysis: Gene Regulatory Motif Identification with A-GLAM Leonardo Mariño-Ramírez, Kannan Tharakaraman, John L. Spouge, and David Landsman 14. Analysis of Genomic DNA with the UCSC Genome Browser Jonathan Pevsner 15. Mining forSNPs and SSRs using SNPServer, dbSNP and SSR Taxonomy Tree Jacqueline Batley and David Edwards 16. Analysis of Transposable Element Sequences Using CENSOR and RepeatMasker Ahsan Huda and I. King Jordan 17. DNA Sequence Polymorphism Analysis Using DnaSP Julio Rozas