HOME |
| GALLERY |
| OVERVIEW |
| FAQ |
| SOURCE |
| CREDITS |
For any questions or suggestions please contact us
GoTo ...
Guidance
FastML
M1CR0B1AL1Z3R
Selecton
ConSurf
Source Code
Please note that the use of the Selecton programs is for academic use only
1. Downloading and compiling Selecton.
2. Running Selecton
Downloading and Compiling Selecton
Note that the source code of selecton is divided into two programs:
- Selecton, which includes the M8, M8a, M5, and M7 models.
- MEC, which includes the MEC model.
Windows
Linux, Unix and other systems
Large datasets (underflow)
Windows
Download and save to your computer the selecton.exe executable file. This is a simple command line application that may be run from MS-DOS. Do not double click on the program from Windows Explorer since this will not work. For the MEC program, downlaod the following executable file mec.exe.
Linux, Unix and other operating systems
1. Download the Selecton source code.
2. In order to unzip and untar the files please type:
tar -xzf selecton.tar.gzThis will create the following directories:
libs/phylogeny3. In some operating systems, you may use the makefiles to compile the program. If this does not work, skip to item 4.
programs/selecton
programs/mec
Make sure you are in the directory where you unzipped the files, and type
cd libs/phylogenyType
makein order to run the Makefile.
Now, type
cd ../../programs/selectonto get to the selecton directory. Type
makein order to run the Makefile.
This will result in an executable file called selecton which will reside in the programs/selecton directory.
Alternativels, to create a MEC executable files, repeat the above steps, replacing programs/selecton with programs/mec.
4. In some systems (such as Unix), the makefiles will not be operable. Thus, follow steps 1-2 and compile directly using g++:
1. cd to the library where you unzipped the files.
2. Type
mv libs/phylogeny/* programs/selecton/3. cd to the selecton library
cd programs/selecton4. To compile, type
g++ -O3 -o selecton *.cppThis will result in an executable file called selecton which will reside in the src/selecton directory.
Perform the same steps to create a mec executable, replacing programs/selecton with programs/mec.
Large datasets (underflow)
For large datasets (typically more than 100 sequences), selecton may suffer from underflow problems.
To bypass this problem selecton can be compiled using an option called doubleRep: In stage 3 above, type "make doubleRep" instead of "make" for both libs/phylogeny and programs/selecton.
This will create a program called selecton.doubleRep, which should be able to handle larger datasets.
Running Selecton
Running Selecton requires 2 steps:
1. Running a codon-alignment procedure, which produces a codon-aligned multiple sequence alignment (for example, you may use the Revtrans server). Alternatively, you can also manually adjust any alignment so it is codon aligned (aligned with triplets of nucleotides).
*** Please note that on alignments which are not codon-aligned (such as DNA or amino-acid alignments run with CLUSTAL and its likes), Selecton will not run.
2. Run Selecton. This is done by typing from the command line, for example:
For windows:
selecton.exe -i seq.aln -u tree.txtFor linux/unix:
selecton -i seq.aln -u tree.txt
Where seq.aln is the codon alignment in fasta/clustal format and tree.txt is a user tree in newick format (non compulsary). For the full list of the parameters type: selecton.exe -h