Table of Contents

Similarity Searching Using BLAST.- Gene Orthology Assessment with OrthologID.- Multiple Alignment of DNA Sequences with MAFFT.- SeqVis: A Tool for Detecting Compositional Heterogeneity Among Aligned Nucleotide Sequences.- Selection of Models of DNA Evolution with jModelTest.- Estimating Maximum Likelihood Phylogenies with PhyML.- Trees from Trees: Construction of Phylogenetic Supertrees Using Clann.- Detecting Signatures of Selection from DNA Sequences Using Datamonkey.- Recombination Detection and Analysis Using RDP3.- CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition.- Genetic Code Prediction for Metazoan Mitochondria with GenDecoder.- Computational Gene Annotation in New Genome Assemblies Using GeneID.- Promoter Analysis: Gene Regulatory Motif Identification with A-GLAM.- Analysis of Genomic DNA with the UCSC Genome Browser.- Mining for SNPs and SSRs Using SNPServer, dbSNP and SSR Taxonomy Tree.- Analysis of Transposable Element Sequences Using CENSOR and RepeatMasker.- DNA Sequence Polymorphism Analysis Using DnaSP.