Python Programming for Biology: Bioinformatics and Beyond

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http://biopython.org

.

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 International  Union  of  Pure  and  Applied  Chemistry;  an  organisation  that  standardises

chemical nomenclature.

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 Felsenstein,  J.  (1993).  PHYLIP  (Phylogeny  Inference  Package)  version  3.5c.

Distributed by the author. Department of Genetics, University of Washington, Seattle.

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Sequence variation and evolution

Contents

A basic introduction to sequence variation

Mechanisms of genetic change

Conservation and variation

Homologues and species

Phylogenetic trees

Similarity measures

Measuring conservation

Conservation display

Calculating substitution matrices

Phylogenetic trees

Phylogenetic trees using neighbour-joining

Tree-guided multiple-sequence alignments

Calculating substitution rates using trees