Toolbox > Overview

Available Software on BBCU server (dapsas)

  • EMBOSS
  • GCG
  • BLAST
  • WU-BLAST
  • FASTA
  • CLUSTALX and CLUSTALW
  • T-Coffee
  • PROBCONS
  • MUSCLE
  • PHYLIP
  • Tree-Puzzle
  • QuickTree
  • HMMER
  • tntblast

    EMBOSS package for Sequence Analysis
    On command line write:
    % EMBOSS program name and press 'Enter'
    Complete list of available programs
    Web access here

    GCG package for Sequence Analysis
    On command line write:
    % gcg and press 'Enter'
    % gcg program name and press 'Enter'
    Complete list of available programs
    Web access on dapsas or on inn

    BLAST package for Database Similarity Searches
    On command line write:
    % blastall -p program name -i query sequence -d database -o output file and press 'Enter'
    for example:
    % blastall -p blastp -i pep -d uniprot -o pep.out and press 'Enter'
    Complete list of available programs

    WU-BLAST package for Database Similarity Searches
    Washington University BLAST is a powerful software package for gene and protein identification, using sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases. On command line write:
    % blasta -p program name -i query sequence -d database -o output file and press 'Enter'
    WU-BLAST Command line options

    FASTA package for Database Similarity Searches and Sequence Alignment
    On command line write:
    % FASTA program name and press 'Enter'
    Complete list of available programs

    CLUSTALX and CLUSTALW programs for global Multiple Alignment of Proteins or DNA sequences
    On command line write:
    (For clustalx you need x-window interface)
    % clustalx and press 'Enter' or
    % clustalw and press 'Enter'

    Note: Both programs are available for PC/Mac

    T-Coffee
    T-Coffee is a multiple sequence alignment package for Proteins or DNA sequences.
    How Does T-Coffee Work
    T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It also allows to estimate the level of consistency of each position within the new alignment with the rest of the alignments.

    To run on dapsas
    On command line write:
    % t_coffee and press 'Enter'
    User Manual (pdf) for T-Coffee is available here

    PROBCONS
    PROBCONS is a novel tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS has achieved the highest accuracy of all alignment methods to date.

    To run on dapsas
    % probcons and press 'Enter'

    User Manual (pdf) for PROBCONS is available: here

    MUSCLE
    is a program for multiple sequence comparison by log-expectation.

    To run on dapsas
    % muscle and press 'Enter'

    PHYLIP software package for Inferring Phylogenies
    On command line write:
    % PHYLIP program name and press 'Enter'
    Complete list of available programs

    Tree-Puzzle
    TREE-PUZZLE is a program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREEPUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated with and without the molecular-clock assumption.

    To run on dapsas
    On command line write:
    % puzzle and press 'Enter'
    User Manual (pdf) for Tree-Puzzle is available here

    QuickTree
    QuickTree is a program for the rapid reconstruction of phylogenies by the Neighbor-Joining method.

    To run on dapsas
    On command line write:
    % quicktree and press 'Enter'
    QuickTree paper is available here

    HMMER
    profile HMM (hidden Markov models) methods for sensitive database searches using multiple sequence alignments as queries.

    HMMER userguide in pdf is available here

    tntblast
    ThermonucleotideBLAST is a program for searching a target database of nucleic acid sequences using an assay specific query. ThermonucleotideBLAST queries are based on biochemical assays (i.e. a pair of oligonucleotide sequences representing PCR primers or Padlock probes, a triplet of oligos representing PCR primers and a TaqManTM probe or a single oligo representing a hybridization probe). Unlike existing programs (e.g. BLAST) which use heuristic measures of sequence similarity for identifying matches between a query and target sequence, ThermonucleotideBLAST uses physically relevant measures of sequence similarity -- free energy and melting temperature. For example, given a pair of PCR primers, a database of DNA targets and an annealing temperature, ThermonucleotideBLAST will return a list of predicted amplicons that will (ideally) match experimental PCR results. To enable searching of very large sequence databases (i.e. all of Genbank),

    To run on dapsas
    On command line write:
    % tntblast -help and press 'Enter'
    A list of all the program's parameters will be displayed.