I am trying to run a DNA parsimonial test on just some sample and after attempting to use PHYLIP and PAUP to no avail, my research team and I have come to a road block. We have found a newer program called Mesquite however there are no adequate tutorials on how to run the program. Are there other programs that anyone would recommend or is anyone familiar with the Mesquite program that would be willing to help get us started?
Do you mean that you want to perform parsimony based phylogenetics on DNA sequences? What is the problem with Paup? And why you have decided to use parsimony? It is not the best choice for DNA sequences.
This question comes from a son of a colleague of mine who is going to the University of St. Thomas in Houston, Texas. This is outside of my area of expertise so I thought I would pose it to the group. His answer to your questions are below:
"Forgive me, I am a student in university and I'm currently doing research with one of my professors and right now another student and myself are currently just learning how to use these programs.
When we attempted to use PAUP, it turned out that the program was too outdated to run anymore and the computer was to hold to handle the newer up date of PAUP.
Freon there we tried using PHYLIP; unfortunately neither of us can seem to get the program to recognize any of the sample data we're trying to use. (Upon starting up, the program shows an error message that it cannot find the "infile". Despite several attempts at renaming out documents abs changing the format of the document, PHYLIP is still unable to recognize any of our data).
Since then we have found a program called Mesquite that has so far worked rather well; however, the program direct come with an instruction manual and needless to say the program can be slightly difficult to navigate.
Our professor had asked us to run some parsimony based phylogenetics and I need just some insight on how to work with these programs / which program is the best to use."
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