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Preface vii
Contributors xi
1 Similarity Searching Using BLAST Kit J. Menlove Mark Clement Keith A. Crandall 1
2 Gene Orthology Assessment with OrthologID Mary Egan Ernest K. Lee Joanna C. Chiu Gloria Coruzzi Rob DeSalle 23
3 Multiple Alignment of DNA Sequences with MAFFT Kazutaka Katoh George Asimenos Hiroyuki Toh 39
4 SeqVis: A Tool for Detecting Compositional Heterogeneity Among Aligned Nucleotide Sequences Lars Sommer Jermiin Joshua Wing Kei Ho Kwok Wai Lau Vivek Jayaswal 65
5 Selection of Models of DNA Evolution with jModel Test David Posada 93
6 Estimating Maximum Likelihood Phylogenies with PhyML Stephane Guindon Frederic Delsuc Jean-Francois Dufayard Olivier Gascuel 113
7 Trees from Trees: Construction of Phylogenetic Supertrees Using Clann Christopher J. Creevey James O. McInerney 139
8 Detecting Signatures of Selection from DNA Sequences Using Datamonkey Art F.Y. Poon Simon D.W. Frost Sergei L. Kosakovsky Pond 163
9 Recombination Detection and Analysis Using RDP3 Darren P. Martin 185
10 CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition Jesse Zaneveld Micah Hamady Noboru Sueoka Rob Knight 207
11 Genetic Code Prediction for Metazoan Mitochondria with GenDecoder Federico Abascal Rafael Zardoya David Posada 233
12 Computational Gene Annotation in New Genome Assemblies Using GeneID Enrique Blanco Josep F. Abril 243
13 Promoter Analysis: Gene Regulatory Motif Identification with A-GLAM Leonardo Marino-Ramirez Kannan Tharakaraman John L. Spouge David Landsman 263
14 Analysis of Genomic DNA with the UCSC Genome Browser Jonathan Pevsner 277
15 Mining for SNPs and SSRs Using SNPServer,dbSNP and SSR Taxonomy Tree Jacqueline Batley David Edwards 303
16 Analysis of Transposable Element Sequences Using Censor and RepeatMasker Ahsan Huda I. King Jordan 323
17 DNA Sequence Polymorphism Analysis Using DnaSP Julio Rozas 337
Index 351
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Add Bioinformatics for DNA Sequence Analysis, The storage, processing, description, transmission, connection, and analysis of the waves of new genomic data have made bioinformatics skills essential for scientists working with DNA sequences. In Bioinformatics for DNA Sequence Analysis, experts in the , Bioinformatics for DNA Sequence Analysis to your collection on WonderClub |