BioEdit

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

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/

BOXSHADE

BOXSHADE is a program for creating good looking printouts from multiple-aligned protein or DNA sequences. The program does no alignment by itself, it has to take as input a file preprocessed by a multiple alignment program or a multiple file editor.

URL:ftp://www.isrec.isb-sib.ch/pub/

Circle

Infer RNA secondary structure using the comparative method.
URL:http://taxonomy.zoology.gla.ac.uk/rod/circles/

ClustalW

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

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/

Dambe

It is a general-purpose package for DNA and protein sequence phylogenies, and also gene frequencies.
URL:http://aix1.uottawa.ca/~xxia/software/software.htm

DCSE

DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor. It can be used to edit protein, DNA or RNA alignments. The structure of the molecules can be incorporated in the alignment.

URL:http://rrna.uia.ac.be/dcse/

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/

DNA Club

PC program for Integrated analysis on DNA sequences.

URL: http://softwareseek.progenote.net/downloads/

EMBOSS

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/

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.

URL: http://www.ebi.ac.uk/fasta33/

FreeTree

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

GeneDoc

GeneDoc does sequence alignment editing and shading, as well as secondary structure shading and super family group support.

URL: http://www.psc.edu/biomed/genedoc/

GeneTree

GeneTree is an experimental program for comparing gene and species trees.

URL:http://www.stats.ox.ac.uk/~griff/software.html

HMMER

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.wustl.edu/

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 language which enables the user to tailor the analyses precisely to his or her needs. These include relative rate and ratio tests, several methods of ML based phylogeny reconstruction, bootstrapping, model selection, positive selection, molecular clock tests and many more...

URL: http://www.hyphy.org/

JalView

Graphical multiple alignment editor. Requires Java Virtual Machine.

URL: http://www.jalview.org/

JEMBOSS

Jemboss is developed by the EMBOSS team. The software is free and part of the EMBOSS distribution.

URL:http://emboss.sourceforge.net/Jemboss/

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.

URL:http://www.megasoftware.net/

MFold

Mfold is an RNA and DNA folding package.

URL:http://www.bioinfo.rpi.edu/~zukerm/export/mfold-3.html

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/

PHYLIP

PHYLIP is a free package of programs for inferring phylogenies.

URL: http://evolution.genetics.washington.edu/phylip.html

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.

URL: http://pearl.cs.pusan.ac.kr/phylodraw/

RNA DRAW

It is an integrated program for RNA secondary structure calculation and analysis.

URL: http://www.rnadraw.com/

Readseq

Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences.

URL: http://iubio.bio.indiana.edu/soft/molbio/readseq/

Seaview

SeaView is a graphical multiple sequence alignment editor. It is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW programs to locally improve the alignment.

URL: http://pbil.univ-lyon1.fr/software/seaview.html

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/

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).

URL: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/index.html

Vienna RNA Package

RNA Secondary Structure Prediction and Comparison.

URL: http://www.tbi.univie.ac.at/~ivo/RNA/

WinGene

A tool for the analysis of nucleotide sequences.

URL: http://www.ipw.agrl.ethz.ch/~lhennig/wingene.html

X3DNA

3DNA is a versatile package for analyzing and rebuilding three-dimensional nucleic acid structures, based on a standard reference frame.

URL: http://rutchem.rutgers.edu/~xiangjun/3DNA/

Artemis

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/

Chromas

It will display and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF, Li-Cor and Visible Genetics OpenGene sequencers can create.

URL: http://www.technelysium.com.au/chromas.html

GenAl

GenAl is a program for genomic alignment, i.e. alignment of DNA sequences with coding regions. It is an implementation of the heuristic algorithm described in Hein, J. & J. Stoevlbaek (1994): Genomic Alignment. J. Mol. Evol.

URL: ftp://ftp.ebi.ac.uk/pub/software/unix/

Glimmer

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/

Glimmer M

A gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programming algorithm that considers all combinations of possible exons for inclusion in a gene model and chooses the best of these combinations. The decision about what gene model is best is a combination of the strength of the splice sites and the score of the exons generated by an interpolated Markov model (IMM).

URL: http://www.tigr.org/software/glimmerm/

MUMmer

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.

URL: http://www.tigr.org/software/mummer/

pDRAW

pDRAW32 is being developed as a free time hobby project. It is far from finished, but as it has reached a point where it could be helpful for many labs, it is now available to the scientific community.

URL:http://www.acaclone.com/

PrimerDesign

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/

Sequin

Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissions containing long sequences, multiple annotations, segmented sets of DNA, or phylogenetic and population studies.

URL: http://www.ncbi.nlm.nih.gov/Sequin/

Staden

The Staden Package consists of a series of tools for DNA sequence preparation (pregap4), assembly (gap4), editing (gap4) and DNA/protein sequence analysis (spin).

URL: http://staden.sourceforge.net/

ADVICE

Automated Detection and Validation of Interaction by Co-Evolution (ADVICE) takes a list of protein sequences or sequence pairs as input and uses orthologous sequences to assess the similarity in the evolutionary history of the proteins. It is suggested that co-evolution of proteins is useful for predicting and validating protein-protein interactions.

URL: http://advice.i2r.a-star.edu.sg/

ANTHEPROT

ANTHEPROT (ANalyse THE PROTeins) is to integrate into a single package most of the methods designed for protein sequence analysis.

URL: http://antheprot-pbil.ibcp.fr/

CNplot

CNplot is a network visualization tool that can be used for large-scale networks, as long as they are pre-clustered.