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Evolutionary relationships between species are usually inferred throughphylogenetic analysis, which provides phylogenetic trees computed from allelicprofiles built by sequencing specific regions of the sequences and abstractingthem to categorical indexes. With growing exchanges of people and merchandise,epidemics have become increasingly important, and combining information ofcountry-specific datasets can now reveal unknown spreading patterns. Thephylogenetic analysis workflow is mainly composed of four consecutive steps,the distance calculation, distance correction, inference algorithm, and localoptimization steps. There are many phylogenetic tools out there, however mostimplement only some of these steps and serve only one single purpose, such asone type of algorithm. Another problem with these is that they are often hardto use and integrate, since each of them has its own API. This project resulteda library that implements the four steps of the workflow, and is highlyperformant, extensible, reusable, and portable, while providing common APIs anddocumentation. It also differs from other tools in the sense that, it is ableto stop and resume the workflow whenever the user desires, and it was built tobe continuously extended and not just serve a single purpose. The timebenchmarks conducted on this library show that its implementations of thealgorithms conform to their theoretical time complexity. Meanwhile, the memorybenchmarks showcase that the implementations of the NJ algorithms follow alinear memory complexity, while the implementations of the MST and GCPalgorithms follow a quadratic memory complexity.

Library of efficient algorithms for phylogenetic analysis