Mercurial > repos > jjv_bioinformaticians > phylogeny_maximum_parsimony_informative_sites

- Tool: Phylogeny Maximum Parsimony
- Autors: J.A. Bernabé Díaz, M.V. Díaz Galián and J.A. Vera Ramos.

- Necessary files:
To run this tool is necessary to have Perl language and Bioperl libraries installed in the system.

- Example of execution:
To execute our code, it is essential to know that the program manages one mandatory argument and two optional ones.
The first of them is the fasta file that contains the sequences that the user wants to analyze, the second and third one contain the number of different values and its repeats, respectively.

Output files:

	Without informative sites:

		Text file "treePars.txt": it contains the tree as text.
		Philip file "sequences.aln": the output of ClustalW.
		Creation of the "images" folder: the plotfile will be placed inside of this directory.

	With informative sites

		Same features from above.
		Philip file "sequences.aln.phy": the output of our "preprocess" subroutine.

According to this, the program can be run with parsimony and without it to check how different the output is. This is shown in the following examples:

# Informative sites disabled.
$ perl phylo-protpars.pl sequences.fasta
$ cat treePars.txt # tree as text
(2134442,(((1170835,1172622),1169853),1708266)); #Result

# Informative sites enabled , num. values = 2, num. repeats = 2.
$ perl phylo-protpars.pl sequences.fasta 2 2
$ cat treePars.txt
(2134442,(1172622,(1169853,(1170835,1708266)))); #Result
author	jjv_bioinformaticians
date	Wed, 12 Apr 2017 11:39:43 -0400
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