Search Software

  • AbokiaBLAST is a parallel implementation of NCBI BLAST created by the inventors of the open-source mpiBLAST project. AbokiaBLAST inherits the super-scalable architecture from mpiBLAST but is re-factored and re-engineered to offer production quality.

  • The Automated Mass Spectral Deconvolution and Identification System (AMDIS) is a computer program that extracts spectra for individual components in a GC/MS data file and identifies target compounds by matching these spectra against a reference library.

  • CLC Genomics Workbench (CLCGWB) is a cross-platform desktop application and graphical user interface for visualizing and analyzing next-generation sequencing data.

  • "CMfinder is a RNA motif prediction tool. It is an expectation maximization algorithm using covariance models for motif description, carefully crafted heuristics for effective motif search, and a novel Bayesian framework for structure prediction combining folding energy and sequence covariation.

  • CREST (Clipping Reveals Structure) is a new algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data. Publication: http://www.ncbi.nlm.nih.gov/pubmed/21666668

     

  • Lasergene Core Suite is a comprehensive DNA, RNA, and protein sequence analysis software suite comprised of ten applications which include functions ranging from sequence assembly and SNP detection, to automated virtual cloning and primer design, to creating publication-quality illustrations of y

  • DOTUR is a computer program that takes a distance matrix describing the genetic distance between DNA sequence data and assigns sequences to operational taxonomic units (OTUs) using either the furthest, average, or nearest neighbor algorithms for all possible distances that can be described using

  • FIRE is a motif discovery component of IGET. The software is available at: https://tavazoielab.c2b2.columbia.edu/FIRE/

  • Galaxy is a web-based platform for data intensive biomedical research.  Anyone with an account at MSI can access the Galaxy server at galaxy.msi.umn.edu

  • GraphClust can be used for structural clustering of RNA sequences. Especially it can be used for clustering of very large dataset with thousands of RNAs.

    http://www.bioinf.uni-freiburg.de/Software/GraphClust/

  • Graphviz is a free and open source graphing application.  It takes the description of graphs in text format and creates images, so that it can be embedded in presentations, papers etc.

  • "Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs).

  • JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence.

  • "LocaRNA is a package of tools for producing fast and high-quality pairwise and multiple alignment of RNA sequences. It uses a complex RNA energy model for simultaneous folding and sequence/structure alignment of the RNAs.

  • mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST.

  • "The PHYLIPNEW programs are EMBOSS conversions of the programs in Joe Felsenstein's PHYLIP package, version 3.69."

    http://saf.bio.caltech.edu/hhmi_manuals/embassy_apps/phylipnew/

  • QIIME (canonically pronounced ‘Chime’) is a pipeline for performing microbial community analysis that integrates many third party tools which have become standard in the field. 

     

    For more information on Qiime specific tutorials, please refer to:

  • RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

  • "RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST+ suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler."

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    "RNAshapes offers three powerful RNA analysis tools in one single software package:

  • "RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs."

  • Sequencher DNA software for sequencing works including contig assembly, editing, restriction enzyme mapping, heterozygote detection, cDNA to genomic DNA large gap alignment, ORF, motif and SNP analysis

  • Software which uses a clustering approach for identification of enriched domains from histone modification ChIP-Seq data.

  • TIBCO Spotfire is a powerful data analysis, visualization and exploration tool, allowing users to quickly identify trends and patterns in data.  It enables quick, interactive data filtering and clear, concise visualizations including bar charts, cross tables, scatter plots and more.

  • trf

    "TRF (Tandem Repeats Finder) is a program to locate and display tandem repeats in DNA sequences."

    Homepage:

    http://www.mybiosoftware.com/sequence-analysis/4083

  • Vector NTI is a bioinformatics software package for DNA and protein sequence analysis.