Bioinformatics links


Sequence analysis

Will Gilbert's sequences analysis package for Mac Os X, (Java)
Emboss
Ebioinformatics, prepackaged Emboss, T-coffee and more for Os X, they also have a Clustal X version for Mac Os X.
Bioteam.net,  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 alignment,  PAL2NAL

(older)

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

    Softberry


    Structural

    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

    Microarrays

    Mark Reimers Microarray info
    Bioconductor
    R-Project for Statistical Computing

    Promoter

    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.

    Varia

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

    Image

    BioImageXD
    Vigra, programming for computer vision



    Links:

    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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