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DAMBE (data analysis in molecular biology and evolution) is an integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data with a user-friendly Windows 95/98/2000/NT interface. DAMBE is free and can be downloaded from http://web.hku.hk/~xxia/software/software.htm. The current(More)
We introduce a new index to measure substitution saturation in a set of aligned nucleotide sequences. The index is based on the notion of entropy in information theory. We derive the critical values of the index based on computer simulation with different sequence lengths, different number of OTUs and different topologies. The critical value enables(More)
Since its first release in 2001 as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution (DAMBE) has gained many new functions that may be classified into six categories: 1) sequence retrieval, editing, manipulation, and conversion among more than 20 standard sequence formats including MEGA, NEXUS, PHYLIP,(More)
Title Type data analysis in molecular biology and evolution PDF computer simulation and data analysis in molecular biology and biophysics an introduction using r biological and medical physics biomedical engineering PDF malaria parasites comparative genomics evolution and molecular biology PDF human mitochondrial dna and the evolution of homo sapiens(More)
Amino acids interact with each other, especially with neighboring amino acids, to generate protein structures. We studied the pattern of association and repulsion of amino acids based on 24,748 protein-coding genes from human, 11,321 from mouse, and 15,028 from Escherichia coli, and documented the pattern of neighbor preference of amino acids. All amino(More)
The relative contribution of mutation and purifying selection to transition bias has not been quantitatively assessed in mitochondrial protein genes. The observed transition/transversion (s/v) ratio is (μ s P s)/(μ v P v), where μ s and μ v denote mutation rate of transitions and transversions, respectively, andP s andP v denote fixation probabilities of(More)
Adaptation to novel environments usually entails morphological changes. The cell morphology of six experimental populations of Pseudomonas pseudoalcaligenes and their common ancestor were examined with scanning electron microscopy (SEM). The six experimental populations were propagated under different temperatures for 10 months: three of them cultured at(More)
Abstract In this paper, we report the thermal adaptation of Pseudomonas pseudoalcaligenes, characterized as changes in growth parameters. Six clones derived from a single colony of P. pseudoalcaligenes were cultured in two different temperature regimes for 10 months, with three clones forming the control group, cultured at a constant temperature, and(More)
We studied 10 protein-coding mitochondrial genes from 19 mammalian species to evaluate the effects of 10 amino acid properties on the evolution of the genetic code, the amino acid composition of proteins, and the pattern of nonsynonymous substitutions. The 10 amino acid properties studied are the chemical composition of the side chain, two polarity(More)