MissMax: alignment-free sequences comparison with mismatches through filtering and heuristics
MissMax is a tool for computing sequence similarity between N genomic sequences and can be used for phylogenetic tree reconstruction. MissMax was developed with the support of the Italian Ministry of Education, University and Reasearch Research within the Project of National Interest PRIN 20122F87B2 ``Compositional Approaches for the Analysis and Mining of Omics Data", PI Cinzia Pizzi
MissMax compute the similarity between two sequences can be based on their average or longest common match when up to k mismatches are allowed. The tool implements both the exact algorithm and the heuristics as described in the paper.
The exact algorithm is way faster than the naive. The heuristic mode is even faster. Of course, it is not guaranteed that the exact distance between the two sequences is computed, but the difference is very small, and in our experiments the quality of the reconstructed tree is not affected.
Download
MissMax was implemented by Cinzia Pizzi and it is freely available, as it is, for academic use at
MissMax download
Contact address: Cinzia Pizzi.
References
If you use MissMax, please cite:
C.Pizzi:
MissMax: alignment-free sequences comparison with mismatches through filtering and heuristics
Algorithms for Molecular Biology, 2016, 11:6
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C.Pizzi:
A filtering approach for alignment-free biosequences comparison with mismatches
In proceedings of WABI 2015, LNCS 9289, pp 231-242
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