# HG changeset patch
# User jjv_bioinformaticians
# Date 1492011583 14400
# Node ID 549887e3f04505a64f724c2f9a4811244767eaa5
# Parent  1cd1d417114201f871b5fb4f9e002e577ca7b20c
Uploading readme.txt

diff -r 1cd1d4171142 -r 549887e3f045 README.txt
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+- 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
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