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Bio Tools
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.
URL: http://www.sanger.ac.uk/Software/Artemis/

BioEdit is a full integrated sequence/alignment editor. Performs translations, phylogenetic analysis, clustalw alignments, ABI trace analysis, RNA comparative analysis and BLAST searches.
URL: http://www.mbio.ncsu.edu/BioEdit/bioedit.html

BLAST 2.0, (Basic Local Alignment Search Tool), provides a method for rapid searching of nucleotide and protein databases.
URL: ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/

CD-HIT is a program for clustering large protein database at high sequence identity threshold. The program removes redundant sequences and generate a database of only the representatives.
URL: http://www.bioinformatics.org/cd-hit/

Clustal-W is a multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results.
URL: ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/

ClustalX is a new windows interface for the ClustalW. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results.
URL: ftp://ftp.ebi.ac.uk/pub/software/dos/clustalx/

DNA Tools
DNATools 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.
URL: http://www.crc.dk/dnatools/

EMBOSS, The European Molecular Biology Open Source Software Suite, is a package of high-quality FREE Open Source software for sequence analysis.
URL: http://emboss.sourceforge.net/

The FastA program has been developed by Pearson & Lipman (1988) and is useful to find all protein sequences of a database such as Swiss-Prot, that are homologous to a given sequence.
URL: http://www.ebi.ac.uk/fasta33/

Freeware program for construction and bootstrap (and jackknife) analysis of phylogenetic trees from binary data (RAPD, RFLP, AFLP etc.)
URL: http://www.natur.cuni.cz/~flegr/programs/freetree.htm

A system for finding genes in microbial DNA, especially the genomes of bacteria and archaea.Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
URL: http://www.tigr.org/software/glimmer/

Glimmer HMM
A fast and accurate gene finder based on a GHMM architecture,
developed specifically for eukaryotes. It incorporates splice site models adapted from the GeneSplicer program and uses interpolated Markov models for evaluating the coding regions.
URL: http://www.tigr.org/software/GlimmerHMM/
 A profile hidden Markov model that can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.
URL: http://hmmer.janelia.org/

Graphical multiple alignment editor. Requires Java Virtual Machine.
URL: http://www.jalview.org/

MEGA is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.
URL: http://www.megasoftware.net/

NCBI ToolKit
The NCBI Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI.
URL: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/

Open Bable
Open Babel is a project designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry.
URL: http://openbabel.sourceforge.net/

PHYLIP is a free package of programs for inferring phylogenies.
URL: http://evolution.genetics.washington.edu/phylip.html

PhyloDraw is a drawing tool for creating phylogenetic trees. It supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams.
URL: http://pearl.cs.pusan.ac.kr/phylodraw/

Primer Design
Primer Design 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 subsequently 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.
URL: http://www.bioinf-club.com/software/

Rasmol is a molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules.
URL: http://www.umass.edu/microbio/rasmol/index2.htm

Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences.
URL: http://www.ebi.ac.uk/cgi-bin/readseq.cgi/

Sequence Manipulation Suite
The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.
URL: http://bioinformatics.org/sms2/

SPDB Viewer
Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
URL: http://au.expasy.org/spdbv/

TreeView X is an open source program to display phylogenetic trees. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs).
URL: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/index.html


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