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