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HOW TO USE PAUP PROGRAM -

PHYLOGENETIC ANALYSES USING PARSIMONY

 

(Swofford, D.L. 1993. PAUP: Phylogenetic Analysis Using Parsimony, Illinois Natural History Survey, Champaign.)  Parsimony methods search for minimum-length trees: trees that minimize the amount of evolutionary change needed to explain the available data.

 

To Set up a PAUP Spreadsheet for Sequence Analysis:

1) under apple menu: seq-example.paup

     An example of a spreadsheet appears.

 

 Edit spreadsheet to your specifications:

ntax= (# of sequences to compare)

nchar= (# of bases in each sequence)

format symbols="gatc." (dot indicates a deleted base. If you have dashes instead, then replace the "." with a "-")

[ITS1 region] (replace in brackets the name of your gene)

 

1) delete out all of the names and sequences

2) type in your sequence names, one under the other

 

To Paste in Sequences:

 

1) double-click on your sequence (text file)

2) click on O.K. (to have it show up in simple text)

3) highlight the whole sequence by clicking mouse at beginning of sequence, hold mouse button down, drag to end of sequence, then let go.  All of the sequence should be highlighted.

4) under edit menu: copy

5) under file menu: quit

6) click on your PAUP spreadsheet

7) click next to sequence name

8) advance at least 6 spaces

9) under edit menu: paste

10) make sure the sequence fits on one line

11) do the same for all of your sequences

 

Make sure all of the sequences are starting and ending together.  All of the sequences must also have the same number of characters.  If there is a shorter sequence, then add N's to the end to make it the same length.  Include "N" in the format symbol list.

 

1) under file menu: save as

2) type in the name of file

3) make sure your folder is shown at the top

4) click on save

5) under file menu: execute (name of your file)

 

To Make a Phylogenetic Tree:

1) under data menu: define outgroup

2) from the ingroup taxa choices, highlight (click on) the name that has the most variable sequence (which you want as your outgroup)

3) click on to outgroup

4) click on o.k.

5) under search menu: branch and bound

6) click on search

7) click on close when search is done

8) view trees:

1) under trees menu: show trees

 

If more than one tree was generated:

1) under trees menu: compute consensus

2) under trees menu: save trees to file

 

To Do Bootstrapping:

It is best to have the computer randomly make trees between 500 - 100 times to test the reliability of your branches.

1) under search menu: bootstrap

2) number of replicates: type in a number between 100-1000 (your choice)

3) type of search: click on branch and bound

4) click on continue

5) click on bootstrap

6) click on close after bootstrapping was executed (you'll hear a beep)

7) under trees menu: print consensus

 8) under trees menu: save trees to file

 

To Set up a PAUP Spread sheet for RFLP or RAPD analyses:

1) under apple menu: RFLP/RAPD PAUP

2) an example of a spread sheet appears

    ntax= (replace with your number of samples)

    nchar= (replace with the number of 0/1 characters in one sample)

3) delete names and 0/1 characters already there

4) type in your sample names with their appropriate 0/1 characters

5) have at least 6 spaces between the names and the 0/1 characters

6) save file as described above

7) execute file as described above

8) make a tree as described above

 

 

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