Bromham: Reading the Story in DNA 
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FiguresBromham: Reading the Story in DNA
Chapter 6
Origin of species
Or: how do I align DNA sequences?
TechBox 6.1 - Taxonomy
There are many online databases that allow you to enter a species name, or higher taxonomic group, to get information and photographs, and you can click up or down through the hierarchy. Note that all of these databases use slightly different taxonomic systems.
Wikipedia (http://en.wikipedia.org/wiki/): an open-access editable database.
The Tree of Life (http://tolweb.org/): an academic project, currently limited in scope but growing.
Entrez Taxonomy (www.ncbi.nlm.nih.gov/Taxonomy/): all species for which there are sequences on GenBank (which is an awful lot, but not everything: see TechBox 1.1 ).
Case study 6.1 - Barcoding nematodes: what you don’t know can hurt you
This nematode taxonomy database can be found at:
http://nematol.unh.edu
TechBox 6.2 - What is a species?
The international conservation union IUCN publishes the definitive list of species threatened with extinction:
www.iucn.org
TechBox 6.3 - Sequence alignment
There are many freely available alignment programs, here are just three examples. The alignments in this book were all produced using the manual editor Se-Al which is available from:
http://tree.bio.ed.ac.uk/software/seal/
There are many publicly accessible server-based automatic alignment programs, such as:
CLUSTALW - www.ebi.ac.uk/clustalw
T-Coffee - www.tcoffee.org
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