Similarity searching using BLAST / Kit J. Menlove, Mark Clement, and Keith A. Crandall -- Gene orthology assessment with OrthologID / Mary Egan ... [et al.] -- Multiple alignment of DNA sequences with MAFFT / Kazutaka Katoh, George Asimenos, and Hiroyuki Toh -- SeqVis : a tool for detecting compositional heterogeneity among aligned nucleotide sequences / Lars Sommer Jermiin ... [et al.] -- Selection of models of DNA evolution with jModelTest / David Posada -- Estimating maximum likelihood phylogenies with PhyML / Stéphane Guindon ... [et al.] -- Trees from trees : construction of phylogenetic supertrees using clann / Christopher J. Creevey and James O. McInerney -- Detecting signatures of selection from DNA sequences using datamonkey / Art F.Y. Poon, Simon D.W. Frost, and Sergei L. Kosakovsky Pond -- Recombination detection and analysis using RDP3 / Darren P. Martin -- CodonExplorer : an interactive online database for the analysis of codon usage and sequence composition / Jesse Zaneveld ... [et al.] -- Genetic code prediction for metazoan mitochondria with GenDecoder / Federico Abascal, Rafael Zardoya, and David Posada -- Computational gene annotation in new genome assemblies using GeneID / Enrique Blanco and Josep F. Abril -- Promoter analysis : gene regulatory motif identification with A-GLAM / Leonardo Mariño-Ramírez ... [et al.] -- Analysis of genomic DNA with the UCSC Genome Browser / Jonathan Pevsner -- Mining for SNPs and SSRs using SNPServer, dbSNP and SSR taxonomy tree / Jacqueline Batley and David Edwards -- Analysis of transposable element sequences using CENSOR and RepeatMasker / Ahsan Huda and I. King Jordan -- DNA sequence polymorphism analysis using DnaSP / Julio Rozas.
