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Lab_2_PHYLIP - Integrative Biology 200A"PRINCIPLES OF...

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Integrative Biology 200A University of California, Berkeley "PRINCIPLES OF PHYLOGENETICS" Spring 2008 Lab 1: Introduction to PHYLIP What’s due at the end of lab, or next Tuesday in class: 1. Print out of Caminicules outfile and outtrees from pars 2. Print out of Azolla consensus output Introduction Today we will be learning about some of the features of the PHYLIP (PHYLogeny Inference Package) software package. PHYLIP was developed by the famous evolutionary biologist Joe Felsenstein, works on most operating systems, and is available for free online. It is widely used, but slightly less popular than PAUP*. Like Mesquite, PHYLIP is an open source package, and you can make changes yourself if you program in C++. Methods available in the package include parsimony, distance matrix, and likelihood, as well as bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and discrete-state characters. What is PHYLIP? PHYLIP consists of about 30 programs that perform different algorithms on various types of data, and collectively are able to do most things you might want to do when it comes to inferring phylogenies. In PHYLIP, there is a program for each method you might want to use, and each type of data you might want to work with: Molecular sequence methods Program: What it does: protpars protein parsimony dnapars DNA sequence parsimony dnapenny DNA parsimony branch and bound dnamove interactive DNA parsimony dnacomp DNA compatibility dnaml DNA maximum likelihood dnamlk DNA maximum likelihood with clock proml Protein sequence maximum likelihood promlk Protein sequence maximum likelihood with clock dnainvar DNA invariants dnadist DNA distance protdist Protein sequence distance restdist Restriction sites and fragments distances restml Restriction sites maximum likelihood seqboot Bootstrapping/Jackknifing Distance matrix methods Program: What it does: fitch Fitch-Margoliash distance matrix method kitsch Fitch-Margoliash distance matrix with clock neighbor Neighbor-Joining and UPGMA method
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Gene frequencies and continuous characters Program: What it does: contml Maximum likelihood continuous characters and gene frequencies contrast Contrast methods gendist Genetic distance Discrete characters methods Program: What it does: pars Unordered multistate parsimony mix Mixed method parsimony penny Branch and bound mixed method parsimony move Interactive mixed method parsimony dollop Dollo and polymorphism parsimony dolpenny Dollo and polymorphism branch and bound parsimony dolmove Dollo and polymorphism interactive parsimony clique 0/1 characters compatibility method factor Character recoding program Tree drawing, consensus, tree editing, tree distances Program: What it does: drawgram Rooted tree drawing program drawtree Unrooted tree drawing program consense Consensus tree program treedist Tree distance program retree interactive tree rearrangement program Getting ready to use PHYLIP
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Lab_2_PHYLIP - Integrative Biology 200A"PRINCIPLES OF...

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