Lab_5_POY_Clustal - Integrative Biology 200A PRINCIPLES OF...

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Integrative Biology 200A University of California, Berkeley PRINCIPLES OF PHYLOGENETICS Spring 2008 Lab 5: Alignment In this lab we’re going to try to look at the effects of different methods of DNA alignment. We’ll try different settings in ClustalW. We’ll go through how to convert the output from ClustalW to a Nexus file, and how to manipulate that Nexus file. We’ll also use POY, which does alignment and tree searching together. Trying different alignment strategies and seeing how they affect your phylogenetic hypothesis is a great way to add some interest to your project, since it helps explore the question of just how much changes at this step affect the trees you build. Get the sequences You have three options: 1) If you want you can get sequences from the organism that you will be working on for your project. Go to http://www.ncbi.nlm.nih.gov/ search for your organism in the nucleotide data base, and try to find about fifteen sequences of a gene from different organisms that will be useful for your study. Download them to your desktop in FASTA format. 2)If you already know that there is nothing good on genbank (or you’re just in a rush), There’s an example FASTA file of COI sequences from some Cephalopod species that you can download from http://ib.berkeley.edu/courses/ib200a/cephalopod_COI.txt . 3) For the really lazy you can just download the Conus sequence file from http://ib.berkeley.edu/courses/ib200a/sequences.fasta . I won’t hold it against you. ClustalW ClustalW is the most commonly used program for multiple sequence alignments. It works by first doing pairwise alignments of each pair of sequences to calculate distances between them. It uses those distances to derive a tree. That tree then guides the production of the multiple sequence alignment. For this lab, we’re going to access
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Lab_5_POY_Clustal - Integrative Biology 200A PRINCIPLES OF...

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