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Source Code
Please note that the use of the SPARTA programs is for
academic use only
Linux and Unix operating systems
1. Download the SPARTA source code.
2. In order to unzip and untar the files please type:
tar -xvf SPARTA.tar
3. Compile directly using g++:
make sure you have gcc/gcc480 installed on your machine.
a. cd to the library where you unzipped the files.
b. cd to the SPARTA library
4. To compile, type
g++ -o sparta -O3 -std=c++11 *.cpp
This will result in an executable file called sparta which will reside in the
sparta directory.
Running sparta
Running sparta requires 4 arguments in the folowing order:
1. Multiple Sequence Alignment("true MSA")
2. INDELible control file with the phylogenetic tree
3. Full path of output directory
4. Number of repetitions
sparta output
sparta will craete 3 sub directories in your output directory 1 2 and 3, each directory
will include the results of each step in the algorithm.
In addition, the folowing files will be created:
* bestResult.txt - contains the set of the best parameters and the distance in the folowing order:
* indelrate, a, rootlength and distance.
* timeRun.txt - the total time the job took(in seconds).
for example:
sparta SPARTA/example/real_msa.fas SPARTA/example/template_control.txt SPARTA/example/ 1000
The output files should look like the files in the example directory.
For any problems or questions please contact us: TalP@tauex.tau.ac.il.
Hope you enjoy!
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