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A new symmetric-iterative method for multiple alignment of protein sequences is presented. The method can be described as a combination of motif finding and dynamic programming procedures. It uses each sequence as a standard to which all sequences are aligned based on the significant segment pair alignment (SSPA) protocol. Sequences are further matched(More)
Conflicting results often accompany phylogenetic analyses of RNA, DNA, or protein sequences across diverse species. Causes contributing to these conflicts relate to ambiguities in identifying homologous characters of alignments, sensitivity of tree-making methods to unequal evolutionary rates, biases in species sampling, unrecognized paralogy, functional(More)
Structurally neighboring residues are categorized according to their separation in the primary sequence as proximal (1-4 positions apart) and otherwise distal, which in turn is divided into near (5-20 positions), far (21-50 positions), very far ( > 50 positions), and interchain (from different chains of the same structure). These categories describe the(More)
Paired individuals of monogamous animal species often stay in close contact when moving in their home range and can be caught together if sampling is done by a method that does not disrupt their spatial association (e.g., capture of birds by mist nets). We propose a statistical procedure that uses the counts by sex of specimens in a number of samples to(More)
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