Bioinformatics
Software downloads
Free
software for bio-scientists, especially you
get it. and you set it up and use it. These are some good programs, and overall
is available, we concentrates on software for molecular biology for
the commonly used.
Two commonly used archives
of molecular biology software are IUBio Archive, at Indiana
University, and the European Bioinformatics Institute (EBI) software
archive. Internet resource locators (URLs) for these are
EBI at http://www.ebi.ac.uk
or ftp://ftp.ebi.ac.uk/
http://www.ncbi.nlm.nih.gov/
- home site for up-to-date access to Entrez software (databank
lookups), Sequin for publishing your sequence in GenBank, Macaw
(multiple alignment), and others.
http://expasy.hcuge.ch/
- home of SwissProt, ProSite and home to a collection of useful
database analyses functions, especially for protein data.
Free
software highlights
Clustal
sequence alignment : Clustal
provides automatic multiple sequence alignment. The current version
is called Clustal W. It is available at ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW
Entrez
to search genome data : The
Entrez program is used for keyword searches of gene sequence
data and Medline literature. It has been written by the programming
staff at the National Center for Biotechnology Information (NCBI).
http or ftp://ncbi.nlm.nih.gov/
NIH
Image for image analysis : A
very useful Macintosh program for general image analysis is NIH
Image, written by Wayne Rasband. Image can be used to measure
the area, average density, center of gravity, and angle of
orientation of a user defined region of interest. version for MS
Windows, from http://www.scioncorp.com/ .
PHYLIP
for phylogeny analyses : The
widely used Phylogeny Inference Package, PHYLIP programs for
inferring phylogenies. It includes analyses of DNA and protein
sequences, restriction sites, distance matrices and gene
frequencies, quantitative and discrete characters, and plotting of
evolutionary trees. ftp://evolution.genetics.washington.edu
RasMol
for molecular modeling : RasMol
is a widely used, free molecular graphics program for the
visualization of proteins, nucleic acids and small molecules. The
program is aimed at display, teaching and generation of publication
quality image. The home for RasMol is ftp://ftp.dcs.ed.ac.uk/pub/rasmol/
EBI-
Fasta executable: Provides sequence similarity searching
against nucleotide and protein databases using the Fasta programs.
Fasta can be very specific when identifying long regions of low
similarity especially for highly diverged sequences
ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/
SeqPup
for sequence editing : SeqPup,
and its predecessor SeqApp, are biological sequence editor and
analysis programs. They includes links to network services and
external analysis programs. SeqPup is usable on common computer
systems, using the new Java language.
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