Bioinformatics for DNA sequence analysis / edited by David Posada. — New York : Humana, c2009. – (58.17/M592/v.537)

Contents

    Contents
    
    1. Similarity Searching Using BLAST
    2. Gene Orthology Assessment with OrthologlD
    3. Multiple Alignment of DNA Sequences with MAFFT.
    4. SeqVis: A Tool for Detecting Compositional Heterogeneity Among Aligned Nucleotide Sequences
    5. Selection of Models of DNA Evolution with jModelTest
    6. Estimating Maximum Likelihood Phylogenies with PhyML
    7. Trees from Trees: Construction of Phylogenetic Supertrees Using Clann 139
    8. Detecting Signatures of Selection from DNA Sequences Using Datamonkey 163
    9. Recombination Detection and Analysis Using RDP3
    10. CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition
    11. Genetic Code Prediction for Metazoan Mitochondria with GenDecoder 233
    12. Computational Gene Annotation in New Genome Assemblies Using GeneID 243
    13. Promoter Analysis: Gene Regulatory Motif Identification with A-GLAM
    14. Analysis of Genomic DNA with the UCSC Genome Browser
    15. Mining for SNPs and SSRs Using SNPServer， dbSNP and SSR Taxonomy Tree
    16. Analysis of Transposable Element Sequences Using CENSOR and RepeatMasker
    17. DNA Sequence Polymorphism Analysis Using DnaSP
    Index