Compute ACS using the prefix-chopping algorithm for every pair of strings present in a database of strings.
- A modern, C++11 ready compiler such as
g++version 4.8 or higher orclangversion 3.2 or higher. - The cmake build system (Version >= 2.8.11).
- A 64-bit operating system. Either Mac OS X or Linux are currently supported.
- Git version control system
- googletest is included as git submodule.
- libdivsufsort libraries are copied in the directory.
Initialize submodules as below, if they are not already initialized.
git submodule init
git submodule update
Next, Create a build directory. For example,
mkdir build
cd build
Finally, build the executable 'alfred.x'.
cmake ..
make
Place the input sequences into fasta files, with each sequence placed in a separate file, in a directory. Run the program while providing this input directory as -i option, the output file as the -o option, and the number of mismatches to allow is given as -k option. An example is shown below:
build/alfred.x -i data/primates/ -o acs.primates.k3.out -k 3
The above command runs the ACS_k prefix-chopping algorithm for the input files in the directory "data/primates" and produces the output to the file "acs.primates.k3.out". It allows three mismatches, while matching for longest common prefix in the ACS_k computation.
If you want to run with a specific set of input files, then you can run as follows:
build/alfred.x -f data/filex.fa,data/filey.fa -o acs.primates.k3.out -k 3
- Thankachan, S. V., Chockalingam, S. P., Liu, Y., Krishnan, A., & Aluru, S. A greedy alignment-free distance estimator for phylogenetic inference. In Computational Advances in Bio and Medical Sciences (ICCABS), 2015 IEEE 5th International Conference on (pp. 1-1). IEEE. 2015.
- Thankachan, S.V., Chockalingam, S.P., Liu, Y., Apostolico, A. and Aluru, S., 2015. ALFRED: a practical method for alignment-free distance computation. Journal of Computational Biology.
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