Parsimony methods

The program that I use for parsimony (mostly because it is free [gratis] and open source) is the Parsimonator (developed in the Stamatakis lab). You can get the code for it there (search on the page, it is pretty far down) or you can get it on the source code distribution website here.

Compilation

The file that you download will be a zip file (if you get it from the Stamatakis lab website). Once the file is downloaded, it needs to be unarchived. In the folder that is created, you will see some source code, some example files, some Makefiles, and a pdf manual. To compile, you will need the gnu c compiler (or the intel one, and if you don’t know what that is, you most likely don’t have it because you have to buy it). To check to make sure that you have the gnu c compiler, in the terminal, type gcc. When you press enter, you will see fatal error: no input files. This is good, and it means that you have gcc. If all is well, run

make -f Makefile.SSE3.gcc

If it worked, the last thing you will see is

gcc  -o parsimonator-SSE3 axml.o  fastDNAparsimony.o -lm

If you get an error, run

make -f Makefile.SSE3.gcc clean

If you just get errors, then you can try

make -f Makefile.gcc

Once this is all over, you will have a file called either parsimonator-SSE3 or parsimonator.

Running the example

Running the program is very straightforward. The basic command will be

./parsimonator-SSE3 -s 125.phy -n 125.test.run -p 12345

where after -s we have the data file, after -n the name of the analysis and -p. The data file that is being used was in the archive. The format for this file is called extended phylip and looks like

4 10
a ACCAGTGAGG
b ACCGGCAGGG
c GCCGACAGGG
d TCCGACAGTT

The first line has the number of species and the number of sites in the alignment. Then it has each species with white space and then the sequence.

After running the program, the output will be

Parsimonator version 1.0.2 a fast open-source code for builiding DNA parsimony start trees

Released under GNU GPL in June 2011 by Alexandros Stamatakis

Alignment has 29149 sites and 125 taxa

1 randomized stepwise addition order parsimony trees with a couple of SPR moves will be computed

Parsimony tree [0] computed in 2.467648 seconds written to file: RAxML_parsimonyTree.125.test.run.0

The files that you are left with will be RAxML_info.125.test.run and RAxML_parsimonyTree.125.test.run.0. The first file will have the output from above in a file and the second is the resulting parsimony tree. You can open it with the program figtree.

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