Bioinformatics Software

1	4Peaks	helps to visualize and edit DNA sequence
2	AAT package	A tool for analyzing and annotating genomic sequences
3	AiO	for integrating Oligo ordering/Data Base and DNA/Protein programs
4	Aligner	align easily your multiple sequences DNA or protein
5	Alscript	Program to format multiple sequence alignments
6	aminoXpress	A multi-functional biochemistry software package
7	AMOS	A Modular Open-Source software for develop. of open-source whole genome
8	Amplify	Macintosh program for simulating and testing PCRs
9	AnnHyb	for sequence editing, translation, seq. statistics, probe design & analysis
10	Antheprot	analysis of a protein sequence and 3D structure analysis
11	ANTHEPROT	it ANalyse THE PROTeins
12	ApE	Plasmid Editor software that highlights and draws graphic maps
13	ArgusLab	it is a molecular modeling, graphics, and drug design program
14	Artemis	a DNA sequence viewer and annotation tool
15	AutoDimer	use to select PCR primers for primer-dimer and hairpin interactions
16	AutoEditor	for correcting sequencing and basecaller errors using seq. alignment
17	BAMBUS	is the first publicly available genome sequence scaffolding program
18	Biodesigner	it is use to create homologous models of proteins, evaluate, and refine the models
19	BioEdit	sequence alignment editor and sequence analysis program
20	Biostatistics	Biostatistics software
21	BLAST	Basic Local Alignment Search Tool
22	Blast Client	Basic Local Alignment Search Tool and more
23	BOXSHADE	pretty printing of multiple alignments
24	CERVUS	parentage analysis using a likelihood approach
25	Chem2Pac	Computational Chemistry Integrator for Windows
26	Chime Plug-in	It allow you to visualize pdb files over the net
27	CHROMA	displays the alignment using text and background colours, bold and italic
28	Chromas	display and prints chromatogram files from ABI automated DNA seq.
29	ClustalW	a powerful tool to do sequence alignments
30	ClustalX	multiple sequence alignment program
31	Cn3D	Application that allows to view 3D structures, at NCBI
32	Coils	Prediction of coiled coil regions
33	Combiner	a program that predicts gene models using the output from other annotation software
34	Complementor	quickly get the complementary (reversed or not) of your DNA sequence
35	Cutter	get the list of all enzyme restriction sites on your sequence
36	DAGchainer	finds sets of genes found in the same order along two genome
37	Deep View	to analyze compare proteins and their active sites or any other relevant parts
38	Deep Viewer	for analysis of several proteins at the same time
39	DICROPROT	for DICHROism of PROTeins
40	DNA Club	DNA analysis software with too many features
41	DNA for Win	Small-scale DNA sequence analysis
42	DNA for Windows	DNA analysis program, ideal for small-scale sequencing projects
43	DNATools	for analysis of DNA and protein sequences
44	Dnatree	DNA phylogeny teaching program
45	DomainParser	A protein domain partition program
46	Dotlet	A Java applet for sequence comparisons using the dot matrix method
47	DynaFit	for nonlinear least-squares regression on chemical or enzymatic kinetic data
48	ELPH	is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein seq.
49	EMBOSS	European Molecular Biology Open Source Software
50	EQS4WIN Lite	allows thermodynamic equilibrium computation and more
51	ESTScan	It detects and reconstructs coding regions from EST seq.
52	Fast PCR	use to design PCR primers, alignment and repeat sequence searching
53	FASTA, 1	Fast Alignment Search Tool
54	FrameProfileScan	Search a the profiles-entries in PROSITE with a DNA sequence
55	FreeTree	analysis package for TreeView
56	GeneDoc	Multiple sequence alignment editor for MS/Windows
57	GenePalette	genome sequence visualization and navigation
58	Generation X	computer simulation of population genetics
59	GeneSplicer	system for detecting splice sites in the genomic DNA of various eukaryotes
60	GeneTree	program for comparing gene and species trees
61	Genome2D	for the visualization of transcriptome and other customized data sets
62	GenomePrimer	use to select the most unique regions within DNA seq. and design primers
63	G-language	it is Genome Analysis Environment, provides useful genome analysis tools
64	Glimmer	Gene Locator and Interpolated Markov Modeler for finding genes in microbial DNA
65	GlimmerHMM	A fast and accurate gene finder based on a GHMM architecture
66	GoCore	Grouping of Conserved regions
67	gOpenMol	graphics interface to the OpenMol
68	hbqcm	Hexamer Based Quality Control Method a quality control algorithm for DNA sequence
69	Hits	A database devoted to protein domains
70	HMMER	hidden Markov models for biological sequence analysis
71	HyPhy	perform maximum likelihood analyses of genetic sequence data and more
72	ISIS/Draw	chemically intelligent drawing package that draw chemical structures
73	Kinemage	three dimensional viewing of molecules
74	LalnView	for visualizing local alignments between two seq. of protein or nucleic acids
75	loopDloop	for drawing RNA secondary structures in molecular biology
76	Macaw	it locate, analyze, and edit sequences and for multiple alignment
77	Mage, 1	Three dimensional viewing of molecules. Retrieve Windows/Mac
78	MANATEE	gene evaluation and genome annotation tool
79	MB	Advanced DNA Analysis
80	MEGA	an incredible Phylogenetic analysis program
81	MeltCalc	is the ultimate thermodynamic modelling which is use to analyze probes
82	Modeltest	compare the fit of the nested GTR family of nucleotide substitution models
83	MOLMOL	for display, analyze, and manipulate the 3D structure of biological macromolecules
84	MrBayes	for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods
85	Multicoil	Program to predict coiled coil regions in proteins
86	MUMmer	A system for aligning whole genome sequences.
87	NCBI-BLAST	Fast sequence similarity search
88	NDE	NEXUS Data Editor is use to create and edit NEXUS format data files
89	Net-Entrez	for search the various sequence databases and the protein database
90	NetPlasmid	draw colored plasmid maps in a few minutes from your browser
91	NJplot	able to draw any binary tree expressed in the standard phylogenetic tree format
92	NOC	program to model/build, visualize and analysis protein structure and more
93	Octopus	is the merger of Visual BLAST-II and Visual FASTA
94	Oligo Analyzer	to determine primer properties
95	Oligo Explorer	to search primers and primer pairs
96	OligoCalc	calculate primer parameters like Tm, %GC and more
97	ORF Viewer	find ORF regions on DNA sequence
98	PAML	for phylogenetic analyses of DNA or protein sequences
99	PASA	Program to Assemble Spliced Alignments
100	PatSearch	Search PROSITE patterns on your protein sequence
101	PatternFind	Search a protein database with a pattern
102	pdb2pov	it converts pdb formatted files to povray
103	PDBViewer	automated homology modelling
104	pDRAW	DNA analysis software
105	pDRAW32	for annotations, DNA cloning, seq. editing, analysis and more
106	PDVIN	Protein Data Viewer for Windows
107	PHIRE	an algorithmic string-based search on bacteriophage genome sequences
108	PHYLIP	the PHYLogeny Inference Package inferring phylogenies
109	Picky	it identifies probes that are very unique and specific to input sequences
110	PIRATE	is a central repository of open-source bioinformatics prediction programs
111	PopG	it simulates evolution of a single locus
112	PrestoPlot	A 2D plotting tool for Windows
113	Primer3	primers from a DNA sequence
114	PrimerAnneal	can search and visualize where primers will hybridize on DNA template seq.
115	ProfileScan	Search a the profiles-entries in PROSITE with your sequence
116	PromoterDB	Search for promoter sequence by keyword
117	ProSeq	Processor of Seq. for alignment editing and various population-genetic analyses
118	PrositeScan	Search the PROSITE database with your sequence
119	Prospect	A threading-based protein structure prediction system
120	ProtCalc	find statistical, theoretical MW, pI and extinction data from protein sequence
121	Protein Explorer	3D structure of proteins, DNA, RNA and more
122	PSAAM	Protein Sequence Analysis and Modelling package
123	Qmol	A lightweight molecular viewer for Windows
124	RasMol	Software for viewing biomolecules in three dimensions (PDB files)
125	RasTop	is a molecular visualization software for Windows
126	RBSfinder	algorithm to find ribosome binding sites for genes in bacterial and archaeal genomes
127	Redasoft	Visual Cloning program for genetic map drawing and DNA sequence analysis
128	RepeatFinder	system for analysis of repetitive structure of genomic sequences
129	RNAdraw	for RNA secondary structure calculation and analysis
130	R-stat. pack	Statistical computing and graphics software
131	SAPS	Statistical Analysis of Protein Sequences
132	Scion Image	for capture, display, analyze, enhance, measure, annotate & output images
133	SeaView	it allows manually edit the alignment, and to run DOT-PLOT or CLUSTAL
134	SecTrace	draw pictures ready for publication from secondary structure prediction
135	SEE ESE	online tool for identifying and visualizing exon splicing enhancers (ESEs)
136	SeqPainter	Colors amino-acids sequence according to their hydrophobicity
137	SEQtools	for handling and analysis of DNA and protein sequences
138	Seqverter	Sequence conversion program
139	Simpip, Simpow	MSDOS program for simulating EPR spectra
140	Spectrum	read in a data file comprising aligned character arrays and more
141	STING	for display of information about macromolecular structure and sequence
142	STORM	extracts protein sequences after ORF and for automatic analysis of proteins
143	Swiss-PdbViewer	helps to analyse several proteins at the same time
144	TIGR Assembler	for assembly of large sets of overlapping sequence data of small genomes
145	TigrScan	gene finder based on the Generalized Hidden Markov Model framework
146	TinyQuant	for analysis of images obtained by scanning of gels or autoradiographs
147	TipDate	estimate the rate of molecular evolution & time-scale of a phylogeny from dated seq.
148	TMpred	Prediction of transmembrane regions
149	TOPSPOT	2D-PAGE-Package and Tools for creating your own 2D-Database
150	TransTerm	a program that finds rho-independent transcription terminators in bacterial genomes
151	TREECON	draw phylogenetic trees on the basis of evolutionary distances
152	TreeExplorer	for phylogenetic tree
153	Treefinder	computes phylogenetic trees from nucleotide sequences
154	TREEMAP	helps to view the contents of a NEXUS or PHYLIP tree file
155	Tree-Puzzle	draw phylogenetic trees from molecular seq. data by maximum likelihood
156	TreeView	view the contents of a NEXUS, PHYLIP, or other format tree file
157	TWAIN	genefinder to predict genes in two closely related eukaryotic genomes simultaneously
158	UniPro Dpview	for finding and analyzing matches between genomes
159	Unveil	a gene finder based on a 283-state Hidden Markov Model
160	VMD	molecular visualization and analysis program
161	WinGene	it translate the sequence in all reading frames, identify ORFs and more
162	WinPep	for analysis of protein sequences and more
163	Yasara	program for viewing an labeling 3-D structures
164	ZCURVE	for recognizing protein coding genes in bacterial and archaeal genomes