Bioinformatics Centre

Bioinformatics Softwares Tools
WINDOWS	LINUX
RasMol : The best to date 3D program is RasMol, originally developed by Roger Sayle. To use this program it must first be downloaded onto your computer.	Clustal W 1.81: Multiple Sequence Alignment Program [ Clustal W ]
JEMBOSS: Java based GUI for EMBOSS	EMBOSS 2.8.0 : The European Molecular Biology Open Software Suite.
Jemboss-current.zip	EMBOSS/EMBOSS-2.8.0 .tar.gz
	EMBOSS-2.8.0-4.gcc.i386.rpm
	EMBOSS-2.8.0-4.icc.i686.rpm
	JEMBOSS 2.8.0 : Java based GUI for EMBOSS
	EMBOSS-Jemboss-2.8.0-4.gcc.i386.rpm
Clustal X is a powerful multiple sequence alignment program with a user-friendly graphical interface. (Windows 95/98) (543 KB)	Gibbs 9.95 Gibbs Motif Sampler [GIBBS ]
DNATools 6.0 is a comprehensive program package for routine handling and analysis of nucleotide and protein sequences. The program includes functions for batch renaming, editing and annotating sequences, restriction mapping, translation, automated blast search and information retrieval, codon analysis, primer design and ordering and a lot more... DNATools only runs on 32bit Windows based PC's *) and it is not possible to run the program on Macs, Unix and other non-Windows computers	MEME/MAST 3.0.4 MEME (motif discovery tool) and MAST (motif search tool) [ MEME-MAST ]
Amplify v1.2 software is for use in designing, analyzing, and simulating experiments involving the polymerase chain reaction (PCR). Given a template sequence and two primers, it will predict the possible outputs of the PCR, taking into account also weak matches to the target sequence. (260.9 KB)	NCBI BLAST 2.2.5 Basic Local Alignment Tool [ NCBI BLAST ]
Meta-MEME is a software toolkit for building and using motif-based hidden Markov models of DNA and proteins. The input to Meta-MEME is a set of similar protein sequences, as well as a set of motif models discovered by MEME. Meta-MEME combines these models into a single, motif-based hidden Markov model and uses this model to produce a multiple alignment of the original set of sequences and to search a sequence database for homologs(Platform:sun) (332.6 KB)	PHYLIP 3.6a3 Phylogeny Inference Package [ PHYLIP ]
pDRAW32(Freeware DNA cloning, analysis and visualization software.). To run pDRAW32 you need a PC running Windows 95, 98, ME, NT4, 2000, XP. .	Primer3 0.9 PCR primer picking tool [ Primer3 ]
PrimerDesign version 1.10 is a DOS-program to choose primer for PCR or oligonucleotide probes. It is tailored to check known sequences for repeats and unique sequences and subsequencly to create prober primers according to this data. A lot of constrains are available to meet your conditions. It can handle up to 32000 base pairs. Click here to see help (234.7 KB)	QRNA 2.0.1 Prototype non-coding RNA genefinder [ QRNA ]
cn3D: It is an application software used to view 3D structure, sequence, alignment and powerful annotation of protein.	cn3D: It is an application software used to view 3D structure, sequence, alignment and powerful annotation of protein.
PHYLIP 3.6 Beta Version: Phylogeny Inference Package	ReadSeq 1: Reads and writes nucleic/protein sequences in various formats [ ReadSeq ]
iOligo is a state-of-the-art primer design program. Version/File 1.0 (Demo)	Sim4: Program to align cDNA and genomic DNA [ SIM ]
TreeView : Software Tool used to draw a tree diagram with sequence data and binary data.	Wise 2 2.0 : Programs to compare DNA and protein sequences [ Wise 2 ]
Chem2Pac is intended to be a kind of computational chemistry integrator, which has a multiple document interface, a molecular rendering utility, and allows the manipulation of various files.	Bioperl 1.2.3 : Perl tools for bioinformatics, genomics and life science research. [ Bioperl ]
GeneTree is an experimental program for comparing gene and species trees. It is available for both Windows and Apple Macs.Current release is 1.3.0 (4 October 2001) (win95/Nt). (983KB)	GDE: The genetic data enviroment (GDE) is a graphical veiw for manipulating DNA and aminoacid sequences for phylogenetic analysisi. Sequences can be edited and analyzed by many others bioinformatics software in our system. GDElinux.tar.gz (2.4MB) Xview libraries: xview-3.2p1.4-6.i386.rpm (0.5Mb) xview-clients-3.2p1.4-6.i386.rpm (0.4 Mb)
Probe allows one to evaluate atomic packing, either within or between molecules. It generates "contact dots" where atoms are in close contact. (159.6KB)
MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR. The program runs on UNIX and Windows NT/95/98/2000 and is freely available.
RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows. (28.8KB)

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