Software

Recently Published

  • ParConnect – an efficient algorithm to compute connected components in large graphs using the distributed memory parallel systems, based on the Shiloach-Vishkin PRAM algorithm.
  • Parallel Suffix Array Construction – a distributed-memory parallel algorithm for the construction of suffix and LCP arrays.
  • ParBLiSS kmerind – is a library in the Parallel Bioinformatics Library for Short Sequences project (ParBLiSS). Kmerind provides k-mer indexing capability for biological sequence data.
  • Enhanced PSbEC – is a parallel spectrum-based error correction software. It is developed as a generic framework to parallelize any spectrum-based error correction and includes three major optimizations (1) dynamic load balancing , (2) cache optimized array layout, and (3) Use of shared memory threads to facilitate processing of large spectrum.
  • ALFRED and ALFRED-G – is an Alignment Free Distance Estimator software for Phylogenetic Inference.

Older Software

  • CLOSET – CLoud Open SequencE clusTering. This is a map-reduce framework for clustering sequences from metagenomic samples, such as 454 reads.
  • Libpnorm – A C/C++ high performance library for all-pairs computations on Cell-based platforms. It provides excellent efficiency in both single and double precision.
  • Parallel T-Coffee – A parallel multiple sequence aligner based on TCoffee 3.79. The tool can easily handle alignments with hundreds of protein sequences.
  • Redeem – Read error detection in repetitive genomes. The software detects sequencing errors in Illumina reads (might be applicable for other types of next-gen sequencing equipments).
  • Reptile – Short Read Error Correction. The software corrects sequencing errors in short reads (32bp ~ 150bp) generated by next-gen sequencing platforms, e.g. Illumina.
  • TINGe & GeNA – Systems biology framework for gene networks inference and analysis. This parallel software can handle whole genome expression data, and it has been successfully used to reconstruct the largest network of Arabidopsis thaliana to date.
  • Error Correction Evaluation Toolkit – Scripts and utilties to evaluate error correction software for next generation sequencing.