Berkeley INTEGBI 200A - NEXUS files, batch files, Mesquite, R (4 pages)

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NEXUS files, batch files, Mesquite, R

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Lecture Notes


Pages:
4
School:
University of California, Berkeley
Course:
Integbi 200a - Principles of Phylogenetics: Systematics
Principles of Phylogenetics: Systematics Documents

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Integrative Biology 200A Systematics By Nick Matzke Updated by Michael Landis University of California Berkeley Spring 2012 Lab 13 Introduction to Scripting NEXUS files batch files Mesquite R In today s lab we will learn about scripting A script is a simple program that basically assembles a bunch of commands into a list and then executes them in series While everyone likes window based programs for figuring out how to do an analysis the first time what if you have to do the same analysis a dozen times or hundreds of times with slightly differing parameters What if you only do the analysis once a year and have trouble remembering the sequence of commands Scripting can be a huge advantage for a scientist in these situations A word about programming if you re not going to take a bunch of computer science classes the best way to learn programming is to have someone introduce you to the basics and get you over the initial hump The hardest part of learning a program from scratch is figuring out how to do the most basic things An introductory online example can be very useful In general the best strategy is to get something minimal working and go from there In this lab we will attempt to get one simple task working for each of these methods of scripting NEXUS files batch files Mesquite R and Python R is a free general statistics package which you will learn about more in IB200b It is probably a necessary skill for any biologist just for general statistical and data visualization purposes We will just introduce a few of the phylogenetics applications here today Setup 1 Download and install Clustalw 2 Download and install R Assignment For each section email me 1 Describe briefly what each of the major commands in the script is doing 2 Provide the output for any two of the R functions 3 Briefly answer any thought questions Send me comments on whether you got the script to work what additional steps you had to take etc This will improve this lab which is new in the future If



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