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PROGRAM: LocalAli
AUTHOR: Jialu Hu
EMAIL: [email protected]

Copyright (C) <2014>  <Jialu Hu>

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

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Description
This file is README file of the package of LocalAli developed by Jialu Hu.
To guide you quickly starting to use our alignment tool, we structured this README into five parts:
1) PREREQUISITE
2) DOWNLOAD
3) COMPILING
4) OPTION
5) EXAMPLES
Before running this program, you are recommended to read this file carefully.
For easy to explain, we denote $LOCALALI as the path to LocalAli folder.

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PREREQUISITE
1. LEMON Graph Library 1.2.3
The source code is freely available under Boost Software License, Version 1.0 at the website: http://ftp.mi.fu-berlin.de/jhu/LocalAli/lemon-1.2.3.tar.gz
Please first compile the lemon graph library before compiling the code of LocalAli.
Note that this package should be moved to the directory $LOCALALI/include.
2. GoTermFinder
This package is necessary only if you want to use "-analyse" option to analyze the Gene Ontology enrichment of reported alignments.
It can be download at http://search.cpan.org/dist/GO-TermFinder/lib/GO/TermFinder.pm.

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DOWNLOAD
1. Checkout the source code from the project's subversion repository
svn checkout http://localali.googlecode.com/svn/trunk/ $LOCALALI

2. Download datasets and lemon-1.2.3
datsets: http://ftp.mi.fu-berlin.de/jhu/LocalAli/dataset.tar.gz
lemon-1.2.3: http://ftp.mi.fu-berlin.de/jhu/LocalAli/lemon-1.2.3.tar.gz

Download the datasets into the folder $LOCALALI and uncompress it with command:
cd $LOCALALI
tar -zxvf dataset.tar.gz
Download lemon-1.2.3 into the folder $LOCALALI/include/ and uncompress it with command:
cd $LOCALALI/include
tar -zxvf lemon-1.2.3.tar.gz


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COMPILING
The compiler g++-4.6 as well as its higher variants is strongly recommended to compile the source code, but not limited to. Visual Studio 11 is also supported.
The compilation should be done under Linux and Mac OS X with several simple commands as follows:

1. Compile LEMON GRAPH LIBRARY

cd $LOCALALI/include/lemon-1.2.3/
./configure
./make
./make check (optional)
./make install (optional)

2. Compile LOCALALI

cd $LOCALALI
./make MODE=Release
#If you want to compile it in Debug mode, run command:
./make (MODE=Debug)
#The binary code will be in the folder ./$LOCALALI after compilation.

#if you want to compile it with other compilers such as g++-4.7, do it like this:
./make MODE=Release CXX=g++-4.7


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OPTION
You can see the detailed option information with option "-h".
It is noted that there are two options you must specify if you want to run LOCALALI for an alignment task. They are described as follows:

1. -profile
The default file is "./profile.txt", but you can also change the filename and path by "-profile" option.
This file tells the program where to find the input files.
It is expected to be in two-column tab-delimited format.
These lines starting with "#" will be seen as comments.
Each line has one keyword and one value, like this:
$keyword	$value
Using this file, you are allowed to set keywords (folder species layers tree) here.

For example:

--------------BEGIN OF PROFILE--------------
folder ./dataset/3-way/
species Celeg20130707
species Dmela20130707
species Scere20130707
layers  input_blast.txt
tree    tree.txt
--------------END OF PROFILE--------------

The specified filenames which are required by localali are:
./dataset/3-way/Celeg201300707.txt
./dataset/3-way/Dmela20130707.txt
./dataset/3-way/Scere20130707.txt
./dataset/3-way/input_blast.txt
./dataset/3-way/tree.txt

Interactions of each species are in three-column tab-delimited format (INTERACTOR_A INTERACTOR_B score) as follows (the third column is not necessary):
--------------BEGIN OF NETWORK--------------
O43521	Q07820	0.40
P05556	P07948	0.43
P05556	P13612	0.66
P07948	P13612	0.43
2609382	P40763	0.40
P17947	Q15156	0.54
--------------END OF NETWORK--------------

The layered graph will be constructed through these homologous proteins (with evalue <1e-07). It looks as follows (the third column is not necessary):
--------------BEGIN OF HOMOLOGY--------------
P31946	Q20655	9e-146
P31946	P41932	2e-137
P62258	Q20655	5e-121
P41932	P62258	5e-113
Q04917	Q20655	9e-133
P41932	Q04917	1e-126
P61981	Q20655	2e-132
P41932	P61981	8e-129
P27348	Q20655	4e-138
P27348	P41932	2e-132
--------------END OF HOMOLOGY--------------

2. other option in Usage

Usage:
  ./localali -version|-alignment|-analyse|-format [--help|-h|-help]
     [-alpha num] [-beta num] [-extdist1 int] [-extdist2 int]
     [-formatfile str] [-maxext int] [-method int] [-minext int]
     [-numconnected int] [-numseeds int] [-numspecies int]
     [-numspinetries int] [-numthreads int] [-parallel] [-profile str]
     [-resultfolder str] [-score_threshold num] [-seedrep int]
     [-seedsize int] [-seedtries int] [-task int] [-verbose int]
Where:
  --help|-h|-help
     Print a short help message
  -alignment
     Execute the alignment algorithm.
  -alpha num
     Impact factor of the evolutionary rate. Default is 0.2
  -analyse
     Make analysis on the alignment results.
  -beta num
     The second impact factor of the evolutionary rate of interactions. Default is 2.0.
  -extdist1 int
     Distance of neighbors in the search for seeds. Default is 1.
  -extdist2 int
     Distance of neighbors in the search for subnets. Default is 2.
  -format
     Process input or output file into proper format.
  -formatfile str
     Input file which is used to analyse the quality of alignments.
  -maxext int
     Maximal number of the extension. Default is 13.
  -method int
     Specify the method used for verification. LocalAli 1, NetworkBlastM 2. Default is 1.
  -minext int
     Minimal number of the extension. Default is 3.
  -numconnected int
     Number of connected subnetwork. Default is 3.
  -numseeds int
     Number of refined seeds. Default is 400.
  -numspecies int
     Number of the species compared. Default is 3.
  -numspinetries int
     Number of tries for strongly connected spines. Default is 5.
  -numthreads int
     Number of threads. Default is 1.
  -parallel
     Run LocalAli in parallel if it is true. Default is false.
  -profile str
     Configuration of various input parameters. Default is "./profile.txt".
  -resultfolder str
     Configuration of various input parameters.
  -score_threshold num
     Score threshold of subnets which are qualified. Default is 0.2.
  -seedrep int
     Allow protein replicatioin in refined seeds. Default is false.
  -seedsize int
     Size of the seeds. Default is 2.
  -seedtries int
     Number of tries for each refined seeds. Default is 1.
  -task int
     Specify the task of each method. Default is 0.
  -verbose int
     Display standard output levle:0-3. Default is 0.
  -version
     Show the version number.

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EXAMPLES

cd $LOCALALI
mkdir ./result 
# The alignment results will be in this folder.

Perform LocalAli on a test alignment (human-worm-fly) with command:

mkdir ./result/3-way
mkdir ./result/3-way/alignments
set the directory of the dataset in ./profile/profile_test.txt.
./localali -alignment -parallel -numthreads 16 -numspinetries 20 -numspecies 3 -numseeds 2000 -score_threshold 0.3 -resultfolder ./result/3-way -seedtries 2 -minext 3 -maxext 13 -profile ./profile/profile_test.txt -verbose 1 -extdist1 2 -extdist2 2 -seedrep 1 


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END
THANKS FOR READING
If you have any questions regarding to the program, please don't hesitate to contact us through email.