To run the algorithms execute the file "algorithmsInBioinformatics.py" in the folder source/bin.
-h, --help
Show this help message and exit
-a {nw,gotoh,nw3,fengDoolittle,sumOfPairs,upgma,wpgma,nussinov},
--algorithm {nw,gotoh,nw3,fengDoolittle,sumOfPairs,upgma,wpgma,nussinov}
Define which algorithm should be executed. Options are:
- 'nw' for the algorithm of Needleman and Wunsch.
- 'gotoh' for the algorithm of Osamu Gotoh.
- 'nw3' for the Needleman-Wunsch algorithm with three sequences.
- 'fengDoolittle' for the heuristic multiple sequence alignment algorithm by Da-Fei Feng and Russell F. Doolittle.
- 'sumOfPairs' for the scoring of a multiple sequence alignment by Humberto Carrillo and David Lipman.
- 'upgma' or 'wpgma' is a clustering method to generate pylogenetic trees.
- 'nussinov' for the RNA secondary structure prediction algorithm by Ruth Nussinov.
-f INPUTFILE, --inputFile INPUTFILE
Define the file in which the input sequences are defined. It have to be in fasta-format.
-o OUTPUTFILE, --outputFile OUTPUTFILE
Define in which file the output should be written. If not defined, it is written to "outputFile.fas" in the local directory.
-w WEIGHTFUNCTION, --weightFunction WEIGHTFUNCTION
Name of a weight function definde in class PairwiseAligmentHelper.
-gc GAPCOST, --gapCost GAPCOST
Name of a gap function definde in class PairwiseAligmentHelper.
--numberOfSolutions NUMBEROFSOLUTIONS
Define the number of optimal solutions the Needleman-Wunsch algorithm should compute.
--outputFormat {graphML,newickTree}
Define the output format of the output file. This function is only parsed if you choose 'upgma' or 'wpgma' as an algorithm. Default is Newick tree.
--similarityScore SIMILARITYSCORE
Name of a similarity score defined in class PairwiseAligmentHelper.
If you are having issues, please let me know. Mail adress: wolffj[at]informatik[dot]uni-freiburg[dot]de