Scientific Software

(Click on the blue button at left and download the software in its own web page)

Codon Usage

Codons    Codons - RSCU, dinucleotide frequencies, translation into protein and different measurements of codon bias (Fop, Nc, ...).****

 

CodonW  Codon W - Interactive correspondence analysis of codon usage *****

 
Picdi  Picdi - Codon usage analysis. Calculates ICDI index, closely related to Nc and CAI. The major advantaje is that preferred codons knowledge is not needed  ***

Graphic Interfaces

    Cn3D - Helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service   ****

 

scop     SCOP - Structural classification and viewing of proteins  ****

Molecular Evolutionary Genetics and Phylogenies

    DnaSP - Package (Windows) with a lot of utilities, very intuitive   *****

 

     Treeview - An excellent Interface (Windows) in Phylogenetics trees  ****

 

MEGA - Molecular Evolutionary Genetics Analysis. Very good approaches to genetic distances in multiple ways and phylogenetic trees                                                        *****

 

PHYLIP  - The most comprehensive, all imbracing collection of phylogenetic programs, including parsimony, maximum likelihood and distance methods, plus utility programs. Runs on anything.   *****

 
  Joe Felsenstein's list of phylogeny software - Itīs his own list. Only the best . . .*****

Primer Design

      GeneFisher - An Interactive PCR Primer Design  *****

 
  Primer Premier 5 - Designs cross species, pathogenic, allele specific primers at the click of a button. Designs PCR, sequencing and hybridization primers automatically. Supports degenerate, multiplex/nested primer design, sequence translation and restriction enzyme analysis. Available for Windows 95/98/NT/2000 and Power Macintosh OS 9. Only one problem, this software isnīt free.    *****

Multiple Purposes

      EBI -(European Bioinformatics Institute, EMBL Outstation, Hinxton, UK) - No comments needed *****

 

   INCBI - (Irish National Centre for Bioinformatics) - Resources and tutorials  ***

 

    Links at the University of Glasgow - A lot of useful resources mainly focused on phylogenetics trees and sequence alignments  *****

 
  Plasmid Premier 2 - Intuitive software to analyze plasmids and produce publication quality plasmid drawings. Support for restriction enzyme analysis, motifs, features and ORF's. Available for Windows 3.1/95/98/NT. The problem, this software isnīt free.    *****

Population Genetics

   Arlequin - Analysis of Population Genetics Data (Windows)   ****

 

        Virtual FlyLab - Design and Mate Flies, very useful for teaching purposes  ****

Restriction Endonucleases
    WebCutter - Continuous actualized restriction endonuclease database. Search and visualization of restriction endonucleases target sequences in your own nucleotide sequence ****

Sequence Alignments and Analysis

      Clustal X - Multiple sequence alignment, tree building and bootstrapping. Multiple output formats. Widely used since clustal V *****

 

   The Protein Colourer - Pretty tool for colouring amino acid sequences ****

 

BOXSHADE  - Pretty Printing and Shading of Multiple-Sequence Alignments at Institute Pasteur  ****

 

IDENTIFY - Motif-based sequence identification   *****

 

Octopus - A graphical tool for the analysis of BLAST and FASTA results       ****

*****Indispensable

****Really recommended

***Useful        

**Limitated in some features

*Uninstall it

 

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