Exercises
·Unix Introduction
·BLAST
·PERL
·Genbank
·BLAST, GCG
·GCG
·Seqlab
·Synthesis
·MSA
·Paup
·Phylogeny
·Examine


·An editor primer
·A GCG cheatsheet
·Flat2fasta homework
·Dynamic Programming homework
·High scoring words homework
·GCG homework
·Seqlab homework
·Mystery sequence homework
·Paup homework

Make your own Character Matrix!


Given the xerox of many clipping devices provided (I would like to scan it so we have color); do the following:
The full picture is here
Create a matrix of characters for > 10 of the devices. Each character should consist of a single attribute. Consider the differences between characters which are binary versus characters with n states.. Once you complete this matrix, import it into nexus format and thus into paup in order to perform a parsimony search. Create and bootstrap a parsimony search tree.

Here is what my initial spread sheet looked like: (click on it to download the spreadsheet) I then transferred that into a fasta file and finally into something which paup would understand


Created: Wed Sep 15 00:58:22 EDT 2004 by Chuck Delwiche
Last modified: Wed Nov 17 10:52:43 EST 2004 by Ashton Trey Belew.