Partial HGT Detection 1.1 - August, 2011                 
Authors     :       Alix Boc and Vladimir Makarenkov (Universite du Quebec a Montreal)
Description :       This program detects partial horizontal gene transfers (HGT). 
Graphical version : The graphical version of this program will be available soon at www.trex.uqam.ca (option Partial HGT-Detection)
	

Whats new ?
===========
In this version we can specify the number of consecutive windows necessary to validate a transfer. 
The default and optimal value is 3. This feature improve the results.

Requirements
============

With Linux/UNIX :
Perl v5.10.0 or higher
g++ compiler (or any other C++ compiler)


Files in package
================

Partial HGT-Detection-1.0
|
|-- install.sh
|-- partial_hgt.pl
|-- run_hgt.pl
|-- src
|   |-- phylip (3.69)
|   |   |-- Makefile
|   |   |-- neighbor.c
|   |   |-- dnadist.c
|   |   |-- protdist.c
|   |   |-- seqboot.c
|   |   |-- consence.c
|   |   |-- phylip.c
|   |   |-- phylip.h
|   |   |-- cons.c
|   |   |-- cons.h
|   |   |-- dist.c
|   |   |-- dist.h
|   |   |-- seq.c
|   |   |-- seq.h
|   |-- hgt (3.3.1)
|   |   |-- Makefile
|   |   |-- hgt.cpp
|   |   |-- fonctions.cpp
|   |   |-- utils_tree.cpp
|   |   |-- structures.h
|   |-- rf
|   |   |-- Makefile
|   |   |-- rf.cpp
|   |-- phyml (396:449M)
|       |-- (all necessary files)
|       |-- Makefile
|-- denamur
|   |-- speciesTree.new
|   |-- mutU.phy
|-- delwiche
|   |-- speciesTree.new
|   |-- rbcL.phy
|   |-- real_names.txt
|-- exec (empty)

Summary
=======

1) Installation procedure.
2) How to run the Partial HGT-DETECTION program.
3) Options.
4) Input file example.
5) Output file example.

1) Installation procedure :
============================

> tar -zxvf Partial-HGT-Detection-1.0.tar.gz
> cd Partial-HGT-Detection-1.0/
> chmod 755 install.sh
> ./install.sh

All the executable files should be in the "Partial-HGT-Detection-1.1/exec" directory.


2) How to call the Partial HGT-DETECTION program :
==================================================

run :> perl partial_hgt.pl speciesTreeFile=denamur/speciesTree.new geneSequencesFile=denamur/mutU.phy opt_bm=30 opt_st=DNA opt_ss=100 opt_nr=5 opt_m=NJ opt_ss=50

run :> perl partial_hgt.pl speciesTreeFile=delwiche/speciesTree.new geneSequencesFile=delwiche/rbcL.phy opt_bm=30 opt_st=AA opt_ss=100 opt_nr=5 opt_m=PhyML opt_ss=50

Follow the link to see the Phylip format for sequences :
http://evolution.genetics.washington.edu/phylip/doc/sequence.html

3) Options:
============

speciesTreeFile    :  Species tree file name. The species tree should be in the Newick format
geneSequencesFile  :  Gene sequences file name. The sequences should be in the Phylip format
opt_m              :  Tree inference (PhyML or NJ)                            : default NJ 
opt_ws             :  Sliding window size                                     : default=100
opt_ss             :  Step size                                               : default=10
opt_st             :  Sequence type (DNA,Amino acids)                         : default=AA
opt_nr             :  Number of replicates in bootstrap                       : default=10
opt_bm             :  Display transfers with bootstrap support higher than x% : default=60%
opt_ncw	           :  Number of consecutive windows necessary to validate a transfer : default=3
  
4) Examples of input files include :
====================================

Denamur et al. (2000)
|-- denamur_speciesTree.new
|-- denamur_mutU.seq

Delwiche and Palmer (1996)
|-- delwiche_speciesTree.new
|-- delwiche_rbcl.seq
|-- real_names.txt

Phylip format allows only 10 characters for the species name, so the species names in the Delwiche and Palmer example were reduced.
The full names and the corresponding reduced names can be found in the file real_names.txt.

 
5) Output file example :
========================

===================================================================================
| Partial HGT-DETECTION V.1.1 (August, 2011) by Alix Boc and Vladimir Makarenkov |
===================================================================================
Species Tree filename   = denamur/speciesTree.new
Gene Sequences filename = denamur/mutU.seq
Sliding windows size    = 100
Step size               = 50
Number of replicates    = 5
Minimum Bootstrap       = 30
Tree reconstruction     = NJ
Sequence Type           = DNA

======================================================================================================================
|  Interval   |   RF  | Bootstrap | Detected transfers
======================================================================================================================
| [  0 - 100] |   27  |     39%   | **********************
| [ 50 - 150] |   30  |     40%   | *********************
| [100 - 200] |   18  |     31%   | *********************
| [150 - 250] |   20  |     36%   | *********************
| [200 - 300] |   21  |     32%   | **********************
| [250 - 350] |   23  |     33%   | ********************
| [283 - 383] |   21  |     35%   | *********************
======================================================================================================================


Partial HGT detected with bootstrap support higher than 30% : 
================================================================

Transfer  : ECOR51->ECOR57
Bootstrap : 40.0%
Interval  : 0-100

Transfer  : ECOR34->ECOR68
Bootstrap : 40.0%
Interval  : 0-100

Transfer  : ECOR52->ECOR51
Bootstrap : 60.0%
Interval  : 200-300

Transfer  : ECOR51->ECOR57
Bootstrap : 80.0%
Interval  : 250-350

Transfer  : ECOR51->ECOR57
Bootstrap : 40.0%
Interval  : 283-383

Transfer  : ECOR26->ECOR27
Bootstrap : 60.0%
Interval  : 283-383


Overlapping partial HGT detected with bootstrap support higher than 30% and validated over 3 consecutive windows
=================================================================================================================

Transfer          : ECOR34->ECOR68
Average bootstrap : 40.0%
Interval          : 0-100

Transfer          : ECOR52->ECOR51
Average bootstrap : 60.0%
Interval          : 200-300

Transfer          : ECOR26->ECOR27
Average bootstrap : 60.0%
Interval          : 283-383

Transfer          : ECOR51->ECOR57
Average bootstrap : 53.3%
Interval          : 0-100

End of the computation ....
