Bookedited by David Posada.
Contents:
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.