Software

Here you can find the software tools and libraries developed by our group. If you have any questions, please contact the respective authors, or directly Srinivas Aluru.

  • 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.
software.txt · Last modified: 2012/10/09 17:21 by zola