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SVPhylA is a python tool for the calculation of several alignment-free distances for phylogenetics analysis from the most popular alignment-free approaches. Such alignment-free methods basically encode DNA and protein sequences (fasta files) into numerical vectors allowing the calculation of alignment-free distances which may be combined into a consensus/compromise matrix by using algorithms like DISTATIS based on Multidimensional Scaling (MSD), Lineal Principal Component Analysis (PCA) and PCA-Kernel (non-lineal).
In addition, genetic distances derived can be either combined between them or with the alignment-free distances. So far, SVPhylA contain a module to compare tree topologies by using different distance measures as a validation procedure. The statistical validation (bootstrap and jacknife) of the alignment-free trees is being developed
SVPhylA is mostly designed to interact to MEGA (MOLECULAR EVOLUTIONARY GENETICS ANALYSIS).
Features
- Integrated the most relevant alignment-free methods to calculate several types of distance matrixes
- Distances matrices are combined into a single/compromise matrix via multidimenional scaling (DISTATIS)
- The resulting matrix (compromise) is introduced to classical distance-based methods
- Data integration is not only applied to alignment-free distances, genetic distances can be included
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