Zapletal, A. | bioRxiv Science

bioRxiv2020

SoftWipe - a tool and benchmark to assess scientific software quality

Scientific software from all areas of scientific research is pivotal to obtaining novel insights. Yet the quality of scientific software is rarely assessed, even though it might lead to incorrect scientific results in the worst case. Therefore, we have developed an open source tool and benchmark called SoftWipe, that provides a relative software quality ranking of 51 computational tools from diverse research areas. SoftWipe can be used in the review process of software papers and to inform the scientific software selection process.

bioinformatics↗

bioRxiv2019

Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning

The so-called site repeats (SR) technique can be used to accelerate the widely-used phylogenetic likelihood function (PLF) by identifying identical patterns among multiple sequence alignment (MSA) sites, thereby omitting redundant calculations and saving memory. However, this complicates the optimal data distribution of MSA sites in parallel likelihood calculations, as the cost of computing the likelihood for individual sites strongly depends on the sites-to-cores assignment. We show that finding a good sites-to-cores assignment can be modeled as a hypergraph partitioning problem, more specifically, a specific instance of the so-called judicious hypergraph partitioning problem. We initially develop, parallelize, and make available HyperPhylo, an efficient open-source implementation for this flavor of judicious partitioning where all vertices have the same degree. Using empirical MSA data, we then show that sites-to-core assignments computed via HyperPhylo are substantially better than those obtained via a previous na i ve approach for phylogenetic data distribution under SRs.

bioinformatics↗