DeCo - Evolution of gene neighborhoods

How to use DeCo

Installation
If you are lucky the executable program works on your system. Download it, type > chmod +x DeCo
and try
> DeCo DeCo.conf_example
If it does not work you will need to download the source C++ program. Its compilation requires that Bio++ is installed (see the installation intructions) and that you know in which directory it is installed. Then unpack Deco by typing
> tar -zxvf DeCo.tar.gz
> cd DeCo
Then edit the makefile file and go to the line
CFLAGS1 = -O3 -I/usr/include/Bpp/ -L/usr/lib
Change the two /usr in the options to the directory in which Bio++ is installed on your system (it can be /usr/local or somewhere in your home directory for example.
Then type
> make
And you should get the executable file, try
> DeCo DeCo.conf_example

Input
You have to prepare four input files:

the gene tree file, where each gene tree is a line in NHX or Newick format, and the leaves are the extant genes. See an example here.
the genes file contains the correspondance between extant genes and the species they are in: each line contains a species name and a gene name. See an example here.
the species file contains the species tree in Newick format. See an example here.
the adjacency file contains an adjacency (or any kind of other relation) between two extant genes in each line: a line contains two gene names. See an example here.

Then you have to prepare a configuration file. It is a set of lines where each line has two words separated by a space. The first four lines are compulsory and tell where your input files are:
trees_file DIRECTORY_OF_YOUR_GENE_TREE_FILE
genes_file DIRECTORY_OF_YOUR_GENE_FILE
species_file DIRECTORY_OF_YOUR_SPECIES_TREE_FILE
adjacencies_file DIRECTORY_OF_YOUR_ADJACENCY_FILE
Additional lines are optional:
exp_name NAME will tag the output files of your run
directory DIR_NAME will place the output file in directory DIR_NAME
OUTPUT_FORMAT FORMAT FORMAT = 0 or 1, for Newick or NHX, according to your favorite format for the output reconciliated gene tree files
sep CHARACTER choose a character which doesn't appear in your dataset (gene names or species names), by default |, this separator is used to annotate trees nodes in the program
Adj_percentage NUMBER NUMBER is between 0 and 1 and is the probability of taking an adjacency when taking it or not has the same score. Default is 0
Crea COST Cost of an adjacency gain, by default 1
Break COST Cost of an adjacency breakage, by default 1
An example of configuration file can be found here.

Start
Type
> DeCo NAME_OF_YOUR_CONFIG_FILE
Or simply
> DeCo
if your configuration file is called DeCo.conf and it is in the current directory.

Output
DeCo, while running, outputs several information on the screen. At the end of execution, DeCo generates six output files:

DIR_NAME/NAME_OUTPUT_species: the correspondence between ancestral species names defined by DeCo and extant species. It's a multi-column file: species followed by all its descendant extant species
DIR_NAME/NAME_OUTPUT_genes: the correspondence between ancestral genes names defined by DeCo and extant genes. It's a multi-column file: species gene_code followed by all its descendant extant genes
DIR_NAME/NAME_OUTPUT_adjacencies: all the ancestral adjacencies computed by DeCo. It's a 3 columns file: species gene1 gene2. The genes are coded by the number of the tree they belong to, followed by the separator, followed by their id in this tree (the numbers of trees and id in trees are defined by DeCo)
DIR_NAME/NAME_OUTPUT_adjacencies_trees: all the adjacencies trees computed by DeCo presented by classes.
DIR_NAME/NAME_OUTPUT_duplicated_gene_pairs: the genes found by DeCo to have been duplicated at the same time. It's a 3 columns file: species gene1 gene2.
DIR_NAME/NAME_reconcil: contains the reconciled trees generated by DeCo from your trees_file genes trees

Page hosted by the PRABI and LBBE, Last modification July 2012

Contact: Severine dot Berard at univ-montp2 dot fr, or Eric dot Tannier at inria dot fr