Difference between revisions of "Phylogenetics: Parsimony Lab"
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== Part A: Using PAUP* to check your answers for homework #2 == | == Part A: Using PAUP* to check your answers for homework #2 == | ||
* Create a NEXUS data file containing the data for the one DNA site you examined for homework assignment #2. To do this, start PAUP*, cancel the opening dialog box (because you have not created a file to open yet), then select File > New from the main menu to create an empty file. Referring to the description of a nexus [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/labs/paupnexus.html#datablock data block from the previous lab], build a NEXUS file containing 4 taxa and 1 character corresponding to the data in homework assignment #2. Be sure to save the file, giving it a name like homework2.nex. | * Create a NEXUS data file containing the data for the one DNA site you examined for homework assignment #2. To do this, start PAUP*, cancel the opening dialog box (because you have not created a file to open yet), then select File > New from the main menu to create an empty file. Referring to the description of a nexus [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/labs/paupnexus.html#datablock data block from the previous lab], build a NEXUS file containing 4 taxa and 1 character corresponding to the data in homework assignment #2. Be sure to save the file, giving it a name like homework2.nex. | ||
| + | |||
| + | * Execute your new data file to make sure there were no mistakes. If it is still open, you can execute it in PAUP* using the key combination <Ctrl-r>. If it is not open, use File | ||
| + | > Open... to open it again. If your file executes successfully, you should see a line such as the following: | ||
| + | |||
| + | <tt>Processing of file "homework2.nex" completed.</tt> | ||
| + | |||
| + | Note: you are not yet finished setting up the file, but it is always a | ||
| + | good idea to periodically check to make sure PAUP* can interpret the | ||
| + | contents. If you wait too long before doing this check, then you end up | ||
| + | making multiple mistakes and it gets increasingly hard to figure out | ||
| + | how to fix all of them! | ||
| + | |||
| + | __NOEDITSECTION__ | ||
Revision as of 14:07, 28 January 2007
| This article is part of an EEB course. Please do not edit the content of this page without the approval of the course instructor. |
Part A: Using PAUP* to check your answers for homework #2
- Create a NEXUS data file containing the data for the one DNA site you examined for homework assignment #2. To do this, start PAUP*, cancel the opening dialog box (because you have not created a file to open yet), then select File > New from the main menu to create an empty file. Referring to the description of a nexus data block from the previous lab, build a NEXUS file containing 4 taxa and 1 character corresponding to the data in homework assignment #2. Be sure to save the file, giving it a name like homework2.nex.
- Execute your new data file to make sure there were no mistakes. If it is still open, you can execute it in PAUP* using the key combination <Ctrl-r>. If it is not open, use File
> Open... to open it again. If your file executes successfully, you should see a line such as the following:
Processing of file "homework2.nex" completed.
Note: you are not yet finished setting up the file, but it is always a good idea to periodically check to make sure PAUP* can interpret the contents. If you wait too long before doing this check, then you end up making multiple mistakes and it gets increasingly hard to figure out how to fix all of them!
