SwiftLink performs multipoint parametric linkage analysis on large consanguineous pedigrees and is primarily targeted at pedigrees that cannot be analysed by a Lander-Green algorithm based program, i.e. many markers, but larger pedigrees.
ParaAT (Parallel Alignment and back-Translation) is a parallel tool that parallelly constructs protein-coding DNA alignments for a large number of homologs. ParaAT is well suited for large-scale data analysis in the high-throughput era, providing good scalability and exhibiting high parallel efficiency for computationally demanding tasks.
ParaBWT is a new and practical parallelized Burrows-Wheeler transform (BWT) and suffix array construction algorithm for big genome data, which has a linear space complexity with a small constant factor.
MSAProbs is a new and practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. Furthermore, MSAProbs is optimized for multi-core CPUs by employing a multi-threaded design, leading to a competitive execution time compared to other aligners.
CUDASW++ (compute unified device architecture) is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST.
PEANUT is a read mapper for DNA or RNA sequence reads. Read mapping is the process of aligning biological DNA or RNA sequencing reads to a known reference genome.
ERA (Elastic Range), a disk-based suffix tree construction method, which works efficiently with very long strings that are much larger than the available memory.