Bioinformatics links

Sequence analysis

Will Gilbert's sequences analysis package for Mac Os X, (Java)
Ebioinformatics, prepackaged Emboss, T-coffee and more for Os X, they also have a Clustal X version for Mac Os X.,  prepackaged emboss

Multiple sequence alignment, phylogenetics

Utopia/Camera5 multiple sequence alignment program (Os X)
ClustalX for Mac Os X, Note: this version requires your data files to be on the system partition (including the users folders).
TreeviewX, cross-platform Tree Viewer, Mac Os X
Quickalign,  multiple sequence editor for Mac Os X, can work together with ClustalX
Bonsai, multiple sequence alignment, cross-platform (Java)
PFAAT, Protein family alignment annotation tool
MAFFT multiple sequence alignment program, XCED multiple sequence editor
MetaPig, Proalign, phylogenetics and multiple sequence alignment
PAML, compile yourself, MacOsX binary available
Tree Puzzle
PHYML, fast maximum liklihood
MUSCLE, multiple sequence alignment

Software: DnaSP, MEGA, Bioedit, PAUP

Align DNA based on Protein alignment: AA to NA alignmentPAL2NAL


ClustalX 1.83 classic

  • for PHYLIP.
  • for TreeView.
  • for downloading Njprot.
  • for seqpup.
  • for downloading molphy.
  • for downloading clustalw.
  • for downloading dendromaker.
  • phylogenic analysis on multiple processors, Linux

  • Gene Prediction



    RasMol 3D viewer software at bernstein & sons
    Open RasMol
    Protein explorer, RasMol derivative
    Swiss PDB viewer
    PredictProtein Servers by Burkhard Rost: Columbia, EMBL, San Diego,

    Online tools

    Online Restriction mapping
    SignalP 3.0 server, prediction cleavage site for signal peptide sequences for protein export
    Online sequence assembly (CAP), small scale projects.  Cap at Ill State.
    AG BIODV: Software Development for Molecular Biology, promoter analysis tools: Transfac, PromoterInspector, MatInspector


    Mark Reimers Microarray info

    R-Project for Statistical Computing


    Jasper, transcription factor binding sites
    Consite, phylogenetic footprinting, compare two promoter sites
    AlignAce, motif discovery
    MetaMeme, promoter analysis
    FamilyJewels, FamilyRelations II (FRII), graphic viewer for Cartwheel analysis server.


    Mek & Tosj software, EnzymeX, LabManager, 4Peaks...
    Functional sites in proteins: ELM


    Vigra, programming for computer vision


    Mac Os X Hints and tricks

    Tools for multiple aligment links (France)
    Open Directory bioinfo software links
    Protein structure viewers, links
    Bioexchange Software
    UCSC Genome Bioinformatics

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