lumpy is a general probabilistic framework for structural variant discovery.
Spliced Transcripts Alignment to a Reference (STAR) is a software package developed for aligning large RNA-seq datasets.
FLUENT uses a finite volume numerical procedure to solve the differential equations governing fluid flow, as well as conservation of energy and chemical species therein. Both compressible and incompressible flows can be modeled, as can turbulence by way of the k-e turbulence model.
From cp2k.org: CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.
In Galaxy TopHat has been replaced with HiSat or HiSat2. When following Galaxy tutorials replace TopHat commands with HiSat or HiSat2. TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.