• EMBOSS package for Sequence Analysis

    open in new windowComplete list of EMBOSS programs
    Web access to EMBOSS open in new windowhere

  • 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'

    For list of the BLAST programs open in new windowclick here

  • FASTA package for Database Similarity Searches and Sequence Alignment
    On command line write:
    % FASTA program name and press 'Enter'

    open in new windowComplete list of FASTA programs

  • BLAT is an alignment tool like BLAST, but it is structured differently. Blat of DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more.
    open in new windowBLAT command line options
  • CD-hit a fast program for clustering and comparing large sets of protein or nucleotide sequences

    open in new windowCD-hit Users Guide

  • CLUSTALW program for global Multiple Alignment of Proteins or DNA sequences
    Note: Both programs are available for PC/Mac too

  • T-Coffee Omega

    T-Coffee is a multiple sequence alignment package for Proteins or DNA sequences.

    for more details about t_coffee various programs open in new windowclick here

  • MUSCLE

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

    To run on sure:
    % muscle and press 'Enter'

  • MEME Motif-based sequence analysis tools
    For overview of the MEME package click open in new windowhere
  • PHYLIP software package for Inferring Phylogenies

    open in new windowComplete list of available programs

  • HMMER

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

    HMMER ver 3b1 userguide in pdf is available PDF open in new windowHere