Data Analysis in Molecular Biology and Evolution
Data Analysis in Molecular Biology and Evolution introduces biologists to DAMBE, a proprietary, user-friendly computer program for molecular data analysis. The unique combination of this book and software will allow biologists not only to understand the rationale behind a variety of computational tools in molecular biology and evolution, but also to gain instant access to these tools for use in their laboratories.
Data Analysis in Molecular Biology and Evolution serves as an excellent resource for advanced level undergraduates or graduates as well as for professionals working in the field.
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FILE CONVERSION 7
ACCESSING GENBANK OR NETWORKED COMPUTERS
FACTORS AFFECTING NUCLEOTIDE FREQUENCIES 41 1 INTRODUCTION 41
THE MOLECULAR CLOCK AND ITS CALIBRATION
COMMON APPROACHES IN MOLECULAR PHYLOGENETICS
TESTING PHYLOGENETIC HYPOTHESES
FITTING PROBABILITY DISTRIBUTIONS
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A-ending codons accession numbers aligned amino acid sequences arginine assumption chapter codon frequencies codon substitutions codon usage bias codon-based DAMBE dialog box dialog box appears distance method DNA methylation DNA sequences elongation equation estimated evolution expected FASTA format four-fold degenerate sites frequency parameters gamma distribution GenBank GenBank file genetic code genetic distances genome Grantham’s distance Ikemura implemented in DAMBE introns LOCUS name matrix maximum likelihood method maximum parsimony mitochondrial molecular clock molecular sequences mRNA mtDNA mutation negative binomial distribution nonsynonymous codon nonsynonymous substitutions nucleotide substitutions null hypothesis number of substitutions output pair-wise comparisons phylogenetic reconstruction phylogenetic tree Poisson distribution prediction protein protein-coding genes purifying selection rate heterogeneity rate ratio parameters reconstructed ancestral sequences result s/v ratio sample sequence file sequence pairs statistical substitution models substitution pattern substitution rate substitution saturation synonymous codon third codon position topology transition bias translational efficiency transversions tRNA User tree values