Bioinformatic - Sequence Analysis Tools

1. BioEdit BioEdit is a full integrated sequence/alignment editor. Performs translations, phylogenetic analysis, clustalw alignments, ABI trace analysis, RNA comparative analysis and BLAST searches.
2. BLAST BLAST 2.0, (Basic Local Alignment Search Tool), provides a method for rapid searching of nucleotide and protein databases.
3. Circle Infer RNA secondary structure using the comparative method.
4. Dambe It is a general-purpose package for DNA and protein sequence phylogenies, and also gene frequencies.
5. EMBOSS EMBOSS, The European Molecular Biology Open Source Software Suite, is a package of high-quality FREE Open Source software for sequence analysis.
6. FastA 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.
7. FreeTree Freeware program for construction and bootstrap (and jackknife) analysis of phylogenetic trees from binary data (RAPD, RFLP, AFLP etc.)
8. GeneDoc GeneDoc does sequence alignment editing and shading, as well as secondary structure shading and super family group support.
9. GeneTree GeneTree is an experimental program for comparing gene and species trees.
10. HMMER A profile hidden Markov model that can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.
11. HyPhy It intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. HYPHY was designed with maximum flexibility in mind and to that end it incorporates a simple high level programming
12. JalView Graphical multiple alignment editor. Requires Java Virtual Machine.
13. JEMBOSS Jemboss is developed by the EMBOSS team. The software is free and part of the EMBOSS distribution.
14. Mega3 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.
15. MFold Mfold is an RNA and DNA folding package.
16. PHYLIP PHYLIP is a free package of programs for inferring phylogenies.
17. PhyloDraw 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.
18. RNA DRAW It is an integrated program for RNA secondary structure calculation and analysis.
19. Readseq Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences.
20. 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.
21. TreeView 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).
22. Vienna RNA Package RNA Secondary Structure Prediction and Comparison.
23. X3DNA 3DNA is a versatile package for analyzing and rebuilding three-dimensional nucleic acid structures, based on a standard reference frame.