Research Software

Biocuration Group has curated the data for software which is essential for the purpose of research in life science.

Neuroinformatics,Bioinformatics,Cheminformatics,Electron Microscopy Image processing ,Pharmacoinformatics and many more software which is free software to download link is  available and other commercial software purchase link available.

All Research softwares : Bioinformatics, Neuroinformatics, cheminformatics, immunoinformatics,Pharmainformatics,Genomics and proteomics
.NET BioA language-neutral bioinformatics toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists.
AMPHORAMetagenomics analysis software
AndurilComponent-based workflow framework for data analysis
AutoDocksuite of automated docking tools
Biochemical Algorithms Library (BALL)C++ library and framework for molecular modeling and visualization designed for rapid prototyping
BioclipseVisual platform for  chemo - and  bioinformatics  based on the  Eclipse  Rich Client Platform (RCP).
BioconductorR (programming language) language toolkit
BioJavaJava (programming language)
BioMOBYregistry of web services
BioPerlPerl language toolkit
BioPHPPHP language toolkit
BiopythonPython language toolkit
BioRubyRuby language toolkit
EMBOSSSuite of packages for sequencing, searching, etc.
FACSFACS machine output analyzer. Percentage to absolute cell numbers.
GalaxyScientific workflow  and  data integration  system
GenePatternScientific workflow system that provides access to more than 150 genomic analysis tools
GeWorkbenchGenomic data integration platform
GMODToolkit for addressing many common challenges at biological databases.
FastPCR"FastPCR is an integrated tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching". This program can be downloaded and run in PCs.
AutoPrimeAutoprime is a very useful software for designing Reverse Transcription Real Time PCR (Q-RT-PCR) primers that are specific to the exon-intron boundaries.
Primer3 (version 0.4.0)It is a freely available online software for designing primers and probe from a DNA sequence. It’s a very popular software due to avilability of several parametrs to design primers with high specificity and accuracy.
PCR PRIMER DESIGN AND REACTION OPTIMISATIONIt’s a very useful site to learn about the pros and cons of factors affecting PCR.
The PCR SuiteIt’s an online primer designing software, hosted by UCSC, that allows users to design primers specific to various types of templates, viz. overlapping amplicons on a template, primers around SNP (in a GenBank), primers flanking exons and cDNA.
Uniprime2It is a website for universal primer designing.
Primo Pro 3.2Its another online primer designing software. Its notable feature is that it can reduce background noise by exercising check on mispriming on non-target DNA sequence. It also "introduces a batch mode option for high throughput PCR primer design".
MethPrimerIts very useful site for designing primers for methylation PCR (Denatured, single stranded DNA (ssDNA) is modified with sodium bisulfite "followed by PCR amplification using two pairs of primers, with one pair specific for methylated DNA; the other unmethylated DNA").
IDT Antisense DesignTo synthesize antisense oligos for a specific target sequence of interest.
PrimerBLASTExtensively used for designing primer and checking the specificity of a given primer.
Gene Fisher"GeneFisher is an interactive web-based program for designing degenerate primers". The underlying assumption is "assumption that genes with related function from different organisms show high sequence similarity, degenerate primers can be designed from sequences of homologues genes". This assumption "leads to isolation of genes in a target organism using multiple alignments of related genes from different organisms"
PrimerQuestOnline primer designing tool provided by IDT
GenomePRIDE 1.0"GenomePRIDE is primer design program that designs PCR primers or long oligos on an annotated sequence"
RE specific primer desining"PCR Designer for Restriction Analysis of Sequence Mutations"
CODEHOP"The COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP) program is hosted by the Fred Hutchinson Cancer Research Center in Seattle, Washington and designs PCR (Polymerase Chain Reaction) primers from protein multiple-sequence alignments"
Oligos 6.2"The program helps to design primer combinations given one fixed primer"
Primo Pro 3.4A java enabled online primer designing tool.
Primo Degenerate3.4"Primo Degenerate 3.4 designs PCR primers based on a single peptide sequence or multiple alignments of proteins or nucleotides. For degenerate primers, the probability of binding to the target is proportional to the effective concentration of the specific primer"
Oligo.Net"OLIGO Primer Analysis Software is the essential tool for designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes including siRNA and molecular beacons. Based on the most up-to date nearest neighbor thermodynamic data, Oligo's search algorithms find optimal primers for PCR, including TaqMan, highly multiplexed, consensus or degenerate primers. Multiple file batch processing is possible. It is also an invaluable tool for site directed mutagenesis"
AlleleID"AlleleID® is a comprehensive desktop tool designed to address the challenges of bacterial identification, pathogen detection or species identification"
Array Designer 2Its an Oligo and cDNA Microarray Design Software. "It designs probes for SNP detection, microarray gene expression and gene expression profiling. In addition, comprehensive support for tiling arrays and resequencing arrays is available"
LAMP Designer"LAMP Designer designs efficient primers for Loop-Mediated Isothermal Amplification assays, that amplify DNA and RNA sequences at isothermal conditions, eliminating the necessity of a PCR setup".
Beacon Designer"Beacon Designer™ automates the design of real time primers and probes".
NetPrimerIt’s an efficient primer analysis software that can be used for determining the featurs of the secondary structures of the generated primer-sequences.
SimVectorIts "an exceptional tool for drawing publication and vector catalog quality plasmid maps, carrying out restriction analysis and designing cloning experiments"
Primer PremierPrimer Premier is one of the "most comprehensive software to design and analyze PCR primers". Primers can be designed for standard PCR, SNP genotyping assays, Multiplexing assyas, along with checking the secondary structures of the designed primers.
Meth Primer"MethPrimer is a program for designing bisulfite-conversion-based Methylation PCR Primers"
Web PrimerA simple tool for primer desining for PCR or sequencing.
Oligo Analyzer Version 3.1 (IDT)The secondary structures produced by the primer(s) can be checked, along with the Gibbs free energy required to produce these structures can be calculated using online Oligo Analyzer Version 3.1 (of IDT).
OligoAnalyzer 3.1This online tool is provided by IDT for analyzing the properties of the oligos as well as for predicting the likelihood of self and heterodimer formation by oligos.
Oligonucleotide Properties CalculatorCalculates base-count, thermodynamic properties (ΔS & ΔH), Tm, GC% values of a given oligo.
Oligonucleotide Properties CalculatorIt’s a very useful, oligonucleotide proterties calculator. It displays the reverse complementary sequence, physical properties (length, molecular weight, GC%), Tm, Thermodynamic constants and hairpin & self-dimer production by a given primer/ sequence.
UnaFoldThe likelihood of secondary structure formation by the single-stranded target is checked by UnaFold software of IDT (freely available online).
Oligo. Properties Calc.Online tool to calculate several features (physical constants, Thermodynamic constants, hairpin formation etc) of one or a pair of oligo nucleotide sequence(s).
Oligo Tm DeterminationCalculates the melting temperatur of the oligos
RestrictionMapperOnline, freely available tool for mapping restriction endonuclease sites on a DNA sequence.
Webcutter 2.0Another RE site detection software (online, free) for linear and circular DNA.
MapperJava platform based online software to map the RE sites on a target sequence.
NEB CutterThis software is RE site mapper, hosted by New England Biolabs.
Web MapWeb Map software maps the RE sites for a given sequence (circular or linear). It can also produce the reverse complementary of the input sequence, which can be assigned for mapping of RE sites.
GeneCopoeia"GeneCopoeia, Inc. is a US-based manufacturer and provider of genomics and proteomics products and services for academic and governmental research institutes, pharmaceutical and biotechnology industry". "GeneCopoeia offers comprehensive tools for microRNA (miRNA) functional analysis so researchers can detect, express, validate or knockdown microRNA of interest confidently. All known human, mouse and rat microRNA in miRBase covered".
RNAi Atlas"RNAiAtlas provides a siRNA oligonucleotide data from different sources and companies like Dharmacon (ThermoFisher), Qiagen, Ambion, esiRNA for human, and visualize interactions between siRNA oligo and predicted off-target".
Comparative RNA Website and Project"The Comparative RNA Web (CRW) Site disseminates information about RNA structure and evolution that has been determined using comparative sequence analysis".
RNAfold"The RNAfold web server will predict secondary structures of single stranded RNA or DNA sequences. Current limits are 7,500 nt for partition function calculations and 10,000 nt for minimum free energy only predicitions".
RNAhybrid"RNAhybrid is a tool for finding the minimum free energy hybridisation of a long and a short RNA"
miRNAMapmiRNAMap 2.0 is a collection of "experimental verified microRNAs and experimental verified miRNA target genes in human, mouse, rat, and other metazoan genomes"
siRNA Designing-BOCK-iT RNAi DesignerOnline siRNA designing tool from Invitrogen
Prediction of miRNA Targets (Mammals)The tool "searches for predicted microRNA targets in mammals"
E-RNAiRNAi construct designer
miRNA Targets and Expression db"Predicted microRNA targets & target downregulation scores. Experimentally observed expression patterns"
miRNa Body map (Human)"The microRNA body map is a repository of RT-qPCR miRNA expression data and functional miRNA annotation in normal and diseased human tissues"
siRNA Design: How toA short introduction to siRNA Designing Steps
miRNA Target Gene Prediction"This website provides access to 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs"
siRNA Wizard v. 3.1"InvivoGen's siRNA Wizard™ is a software designed to help you select siRNA/shRNA sequences targeting your gene(s) of interest. This program selects siRNA/shRNA sequences that match criteria suggested by studies of RNA interference and which will have the best expression rate in psiRNA vectors.".
siDesign- Thermo Scientific"The siDESIGN Center is an advanced, user-friendly siRNA design tool, which significantly improves the likelihood of identifying functional siRNA.One-of-a-kind options are available to enhance target specificity and adapt siRNA designs for more sophisticated experimental design"
RNAi Explorer- GeneLink-siRNAAdesigning tool for siRNA
RNAi Explorer- GeneLink-shRNAshRNA designing online tool.
BLASTBasic local alignment search tool, provided by NCBI.
Translate a DNA SequenceIt’s a Java based free online software, to translate a given input DNA sequences and display one (at a time ) of the six possible reading frame according to the selection made by the user. It also displays the graphical output for all the six reading frames together.
ORF Finder"The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database".
Ensembl Variant Effect Predictor"This tool takes a list of variant positions and alleles, and predicts the effects of each of these on overlapping transcripts and regulatory regions annotated in Ensembl. The tool accepts substitutions, insertions and deletions as input".
DAVID v. 6.7The Database for Annotation, Visualization and Integrated Discovery (DAVID ) v6.7 “provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes”.
ReadSeq-Sequence Format Conversion ToolOnline tool for conversion of sequence format.
READSEQConverts input DNA/AA sequence to specified output format (Input format is determined automatically).
BioEdit"BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7". One can download and then work with the molecular sequences for alignment, restriction mapping, RNA analysis, translation, graphical viewing of electropherogram etc.
DNA/RNA GC Content CalculatorOne can calculate the GC content of a nucleotide sequence.
PEDANT"The pedant genome database provides exhaustive automatic analysis of genomic sequences by a large variety of bioinformatics tools"
SIDDbase 1.0a.ws1"SIDDbase-WS is a SOAP based Web Service" that "provides interoperable access to the SIDD software, and access to the repository of stored results from calculations previously performed on complete bacterial genomes"
SANBI ToolsAn array of online tools (dPORE-miRNA, TcoF, PROMEX etc) are avilable which are maintained by South African National Bioinformatics Institute.
VBI resourcesThis site of Virginia Bioinformatics Institute maintains several tools for bioinformatics analysis viz. "Analysis of Dynamic Algebraic Models", "Complex Pathway Simulator", "Genome Reverse Compiler" etc.
CINEMA 2.1CINEMA stands for Colour INteractive Editor for Multiple Alignments. It’s a free software for sequence alignment with color editor.
MACAWThis links enables you to download Multiple Alignment Construction & Analysis Workbench (MACAW) software. This program is used for "locating, analyzing, and editing blocks of localized sequence similarity among multiple sequences and linking them into a multiple alignment".
SIM4A stand alone program designed to run on Unix based system. It is used for aligning an expressed DNA sequence with a genomic sequence, allowing for introns.
PILUPIt "creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments. It can also plot a tree showing the clustering relationships used to create the alignment".
JALVIEWIt is a "multiple alignment editor written in Java". It is used in EBI Clustalw, Pfam protein domain database, however, it is "available as a general purpose alignment editor and analysis workbench".
SIMIt is an online "program which finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence".
Clustal Omegathe latest form of Clustal alignment program. It is online and command-line based. The distinguishing feature of Clustal-omega is its scalability, as several thousands of medium to large sized sequences can be aligned simultaneously. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to the previous versions. The algorithm uses seeded guide trees and HMM profile-profile progressive alignments.
Clustal WA very popular site for pairwise and multiple sequence alignment. . It runs in Windows, Linux/Unix and Mac operating systems.
CLUSTAL XLatest version of ClustalX 2.0 is provided by "Plate-Forme Bio-Informatique de Strasbourge", along with detail instructions (help) for operating ClustalX. Besides, this site also provides online tools (ciz. Actin Related Proteins Annotation server, EMBOSS, Gene Ontology Annotation, SAGE experimet parameters, GPAT etc) and database (SRS, BAliBase, InPACT), Documentation (tutorials to elucidate the parameters of Clustal, GCG, EMBOSS, Bioinformatics protocols etc).
LALIGNLalign is considered as one of the most reliable tool for local alignment of nucleotide and amino acid sequences.
LALIGNOnline free tool for finding local alignment between two sequences (provided in stipulated input format, viz. plain text without header line, Swiss-Prot ID, TrEMBL ID, EMBL ID, EST ID etc).
FASTAThis server is hosetd by the University of Virginia, USA. It harbours a multiple online software for sequence (nucleic acid and mino acid) comparison, local and global alignment, Hydropathy plotting and protein secondary structure prediction.
MAFFT version 6"MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences)".
T-cofeeTree-based Consistency Objective Function For alignment Evaluation (T-Coffee) is another popular multiple sequence alignment program, developed by Cedric Notredame, CRG Centro de Regulacio Genomica (Barcelona). It allows combining results obtained from several alignment methods. The URL is The default output format is Clustal, while it accepts sequences in PIR and FASTA format.
Phylogeny Inference Package"PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables".
Phylogeny Inference Package (v. 3.5)"This is a FREE package of programs for inferring phylogenies and carrying out certain related tasks. At present it contains 31 programs, which carry out different algorithms on different kinds of data".
Molecular Evolution Geneti Analysis (v. 5.1 beta)A handy package for analysing sequence data for pair-wise and multiple sequence alignment, phylogenetic tree (include neighbor-joining, maximum parsimony, UPGMA, Maximum likelihood and mimimum evolution based) construction and estimation of evolutionary parameters.
List of phylogenetics softwareList of online/downladable software for phylogenetic tree construction, displayed with links in Wikipedia page.
Expert Protein Analysis System“ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc”.
RASMOL Home page"This site is provided for the convenience of users of RasMol and developers of open source versions of RasMol".
Expasy-Translate toolIt’s an online tool that "allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence".
Protein Data BankPDB is an "information portal to biological macromolecular structure". "The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies".
RASMOLRasMol is a molecular visualization tool for protein in 3-dimension.
Structural Biology Software DatabaseHarbors links to several software for docking
MS UtilsMaintains links to several platforms, pipelines, libraries, software for visualization as well as software for proteomic data analysis,.
Protein Tertiary StructureThis site contains links to several software for "calculating and displaying the 3-D structure of oligosaccharides and proteins. With the two protein analysis sites the query protein is compared with existing protein structures as revealed through homology analysis".
Structural Bioinformatics GroupThis is the structural bioinformatics related page maintained by Imperial College London. This site can be used for several purpose, viz. "analysis of protein structure and function with the aim of deriving evolutionary insights, modelling and comparison of biology networks to provide insights into Systems Biology, modelling of the activity and toxicity of small molecules as an aid to the design of novel drugs".
Promoter 2.0 Prediction ServerPromoter2.0 predicts transcription start sites of vertebrate PolII promoters in DNA sequences. It has been developed as an evolution of simulated transcription factors that interact with sequences in promoter regions. It builds on principles that are common to neural networks and genetic algorithms.
Splice PredictorsA method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models.
GeneMarkGeneMark is a “family of gene prediction programs developed at Georgia Institute of Technology, Atlanta, Georgia, USA”.
HMMgene 1.1 web server"HMMgene is a program for prediction of genes in anonymous DNA". "The program predicts whole genes, so the predicted exons always splice correctly. It can predict several whole or partial genes in one sequence, so it can be used on whole cosmids or even longer sequences".
GASGAS is UNIX or DOS based downloadable, command-line oriented "integrated computer program designed to automate and accelerate the acquisition and analysis of genomic data".
GENSCANGENSCAN is a freely available software used for "identification of complete gene structures in genomic DNA". Genscan can be used "for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms".
GlimmerGlimmer (Gene Locator and Interpolated Markov ModelER) is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
Genome Bioinformatics Research LabThe site harbors"geneid" program which is used to "predict genes, exons, splice sites and other signals along a DNA sequence". This site is also hyperlinked with "Gene prediction on whole genome" which is a "precomputed whole genome prediction data sets".
WebgeneThis site maintails several online "tools for prediction and analysis of protein-coding gene structure".
geneid"geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure".
mgene"mGene is a computational tool for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences".
Ensembl Genome Browser"The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online".
EnsembleEnsemble, a genome browser like NCBI and UCSC, is a centralised repository of the Whole Genome Sequence of human and other species (vertebrate and model organisms).
UCSC Human Genome BrowserIts an interactive genome browser dedicated to human genome sequence.
UCSC Genome BrowserThis is an “on-line genome browser hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations”.
Software wURLdBio-wURLd is a searchable, user-maintained collection of URL's related to bioinformatics, biochemistry, and molecular biology. It comprises biocatalogues, other software or a link enlsiting the bioinformatics software.
Swiss Institute of Bioinformatics"The SIB Swiss Institute of Bioinformatics is an academic, non-profit foundation recognised of public utility". SIB "provides high quality bioinformatics services to the national and international research community".
ExPASY Resource PortalA resource portal supported by Expert Protein Analysis System and Swiss Institute of Bioinformatics for analysing bioinformatics data.
Multi-Proteomics SuiteA site that provides several databases pertaining to conserved proteins, motifs as well as tools for protein structure visualization and motif discovery.
Webserveres developed by Dr. GPS raghava at IMTECH, IndiaA very useful site for obtaining several online tools viz. Genome annotation, Structure prediction, Functional annotation, vaccine design, Databases etc.
Emboss AlignThe European Molecular Biology Open Software Suite (EMBOSS) "is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community". Some of the applications are prophet (Gapped alignment for profiles), infoseq (Displays some simple information about sequences), water (Smith-Waterman local alignment), pepstats (Protein statistics) etc.
geneinfinityThis site contains description and links to various sites pertaining to Protein Secondary Structure. It is a hub for getting a quick look at several servers and metaservers that harbor databases and/or tools for prediction of protein secondary structures.
Genome Tools"The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules".
Bioinformatics Software“Softberry, Inc. is a leading developer of software tools for genomic research”. The various areas covered by this company are: Genome annotation, Functional site identification in DNA and Proteins, Sequence database managing, Genome comparison, Expression data analysis, Protein structure prediction and Protein compartment (destination) prediction.
Bioinformatics programs and databasesA collection (alphabatically arranged) of evaluated bioinformatics programs and databases.
Sequence Manipulation Suite-2A suite available for almost all possible manipulation work that can be done with a given DNA or amino acid sequence, viz. Format change, Sequence splitting, CpG island detection, ORF fnding, Pairwiase alignment, RE-Digestion, in silico mutation etc.
NRSP-8 Bioinformatics Online ToolsExplore and utilize several bioinformatics tools.
Gel Compar II (Paid multimodule, stand alone software)It’s a commercial product. "GelCompar II consists of the Basic Software and 5 modules: Cluster analysis, Identification & Libraries, Comparative Quantification and Polymorphism Analysis, Dimensioning techniques & Statistics, and Database Sharing Tools".
Bioinformatics Links DirectoryIts also a very useful site that harbors the links to all possible sites pertaining to computer (for bioinformatics), molecular sequences, expression, organisms, literature pertaining to bioinformatics etc.
Biological software developped at the Institut PasteurSeveral useful bioinformatics tools have been developed and have been made available to the scientific community. Some of the software are: sequence structure evaluation, NMR calculation, Fast databank entries retriever etc.
BUBS- multi software toolsThe "Bielfeld University Bioinformatics Server" provides several online bioinformatics tools Genome Comparison, Alignments, Primer Design, RNA Studio, Evolutionary Relationships, protein docking, image processing for microarrays etc.
Computational Biology at ORNLThe Computational Biology and Bioinformatics Group of the Biosciences Division of Oak Ridge National Laboratory provides data and bioinformatics tools for prokaryotic and some eukaryotic genome and related analysis. The tools are "Gene Channel", "Generation Microbial Gene Prediction System", "Grail (Microbial Gene Prediction System Internet Linked", "Genome Analysis Pipeline" etc.
Biocomputing TutorialsThe site harbors a number of biocomputationa onlinel tools (Cleaner, Translator, NetPlasmit, Aligner, PatSearch etc for nucleotide and protein sequences) and half a dozens of software.
PROMOTERS & TERMINATORSThis site maintains links for different software and tools (viz. PromScan, SCOPE, Promoser, Arnold, WebGesTer) for scanning, predicting promoters and transcription terminators in Eukaryotes and Prokaryotes.
Multiple tools for alignmentsThis site provides several links for pairwise and multiple alignments.
Galaxy Platform"Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses".
GreenGenes (16srRNA sequence Alignment)The greengenes web application provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools presented by greengenes can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences.
Science for SocietyAn wonderful site that maintains links to several stand-alone, downloadable software as well as online software/tools for proteomics, molecular docking, modelling, chemistry tools, cheminformatics, as well as some databases.
SDSC Biology Workbench"The Biology WorkBench is a web-based tool for biologists. The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems"
CSIR Informatics PortalThis page is maintained by CSIR and harbors the software/tools developed for bioinformatics analysis.
VLS3DThis page maintains a "list of in silico drug design online services, standalone and related databases. It is manintained by Dr. B. Villoutreix, research director at the French National Medical Research Institute (Inserm)"
User:Jarle Pahr/: BioinformaticsThis page harbors several "links and notes regarding bioinformatics". This is a very useful link since a user can get link to almost all aspects of bioinformatics resources.
Gel-Quant softwareThe "Gel-Quant" software is used to analyse one dimensional gel images. The gel image is saved in "bitmap" format, following electrophoresis and scanning the gel.
Gelcompar II V. 7.1For analysing 1D Gel
I-TASSER OnlineI-TASSER is an online bioinformatics platform for predicting protein structure vis-à-vis funtion. It has been developed by Zhang Lab (University of Michigan) . It has topped the in CASP ranking of structure prediction during the years 2007 to 2010.
PHYRE2Protein Homology/AnalogY Recognition Engine (PHYRE) is a non-commercial, very popular online protein structure prediction (homology modelling) server. The user friendly GUI is very helpful for the novice in the field of protein structure prediction.
MODELLERThe homology modeling of Protein 3D structures can be done using downloadable software “MODELLER”. It can also be used for following protein structure based applications: databases search for amino acid sequences, Sequence and structural alignments clustering, de novo modeling of structural loops, model-optimization against user defined objective function and so on.
SwissModelIt is a fully automated protein structure homology-modeling server. One needs to register and then log in to create own work space.
QUARK OnlineIt is online software that applies QUARK algorithm for ab initio protein folding vis-à-vis structure prediction. It is another eminent online tool of Zhang lab that has secured esteemed ranking in CASP
HHPredHomology detection & structure prediction by HMM-HMM: used for sequence database searching and structure prediction. It is fast enough and more sensitive in finding remote homologs. HHpred is performs pairwise comparison of profile hidden Markov models (HMMs). It can produce pairwise query-template sequence alignments, merged query-template multiple alignments & 3D structural models calculated by the MODELLER software from HHpred alignments
RaptorXAnother efficient protein structure prediction server that predicts the secondary & 3D protein structure. Besides, it also predicts solvent accessibility and disordered regions, assigns the following confidence scores to indicate the quality of a predicted 3D model. It has been developed by Xu Group of Toyota Technological Institute at Chicago. RaptorX-Binding, another tool available in the homepage of RaptorX is used for model-assisted protein binding site prediction.
RobettaRobetta (Beta Version) of Baker Lab, Washington, USA, is a full-chain protein structure prediction tool. It can be used both for ab initio and comparative approaches for protein structure prediction.
YASARAYet Another Scientific Artificial Reality Application (YASARA) is used for predicting the rotamers (protein side-chain conformations) starting with single point mutations to complete homology models of proteins.
Statistical Analysis of Protein Sequences (SAPS)It performs several statistcialanalyis of the physiochemical properties and other features of the protein sequenc, viz. compositional analysis, charge distributional analysis, distribution of other amino acid types, repetitive structures, multiplets, periodicity analysis
Protscale"ProtScale allows you to compute and represent the profile produced by any amino acid scale on a selected protein".
Bioinformatics Tools for Protein Structure AnalysisHarbors links to several bioinformatics tools for protein structure prediction and visualization.
Mobyle 1.5This site maintains a number of online bioinformatics programs (assembly, database, display, hmm, phylogeny, protein, sequence, structure etc), workflows (alignment, db, phylogeny) and tutorial
ModbaseIt’s a database for "comparative protein structure models". The pipeline used is ModPipe.
SIMPA96 Secondary Structure PredictionAn online to predict secondary structure of protein
SOPMAIts an online protein Secondary structure prediction tool
DeepView: SWISS PDBViewer v. 4.1"Swiss-PdbViewer (aka DeepView) 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"
WHA T IFWhat If "is a versatile molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc". The web interface provides a number of tools viz. Structure validation, Analyse a residue, Protein analysis, 2-D graphics, 3-D graphics, Hydrogen (bonds), Rotamer related, Docking, Crystal symmetry, mutation prediction etc.
SWISS Model"SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists worldwide"
Compute pl/MwThe tool "compute pI/Mw is a tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of UniProt Knowledgebase (Swiss-Prot or TrEMBL) entries or for user entered sequences"
Peptide MassThis online tool of ExPASy "PeptideMass cleaves a protein sequence from the UniProt Knowledgebase (Swiss-Prot and TrEMBL) or a user-entered protein sequence with a chosen enzyme, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the protein of interest"
ProtParam"ProtParam is a tool which allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY) "
Secondary Structure Prediction Tools"These are a collection of protein secondary structure analysis and information sites"
CPHModels 3.2 Server"CPHmodels 3.2 is a protein homology modeling server. The template recognition is based on profile-profile alignment guided by secondary structure and exposure predictions"
EsyPred3D"ESyPred3D is an automated homology modeling program. The method gets the benefit of the increased alignment performances of an alignment strategy that uses neural networks".
Mol. Modelling Database (MMDB)It harbors "experimentally resolved structures of proteins, RNA, and DNA, derived from the Protein Data Bank (PDB), with value-added features such as explicit chemical graphs, computationally identified 3D domains (compact substructures) that are used to identify similar 3D structures, as well as links to literature, similar sequences, information about chemicals bound to the structures"
Drug DesigningThis webpage maintains several entries to drug-designing. One can learn, and make use of these software/ links.
Click2Drug"Click2Drug contains a comprehensive list of computer-aided drug design (CADD) software, databases and web services. These tools are classified according to their application field, trying to cover the whole drug design pipeline".
DRUG DESIGN APPS FOR SMART PHONEA wonderful site that harbors a number of drug designing applications for smart mobiles.
Computational Resources for Drug Discove"CRDD (Computational Resources for Drug Discovery) is an important module of the in silico module of OSDD. The CRDD web portal provides computer resources related to drug discovery on a single platform. Following are major features of CRDD".
FASTX Tool KitThe FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
The Genome Analysis Toolkit (GATK)“The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it’s a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner”.
Genome-wide Complex Trait Analysis (GCTA)"GCTA (Genome-wide Complex Trait Analysis) is designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits".
Burrows Wheeler Algorithm Download"BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads".
SAM Tools"SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format".
BFASTBFAST stands for "Blat-like Fast Accurate Search Tool ". "BFAST facilitates the fast and accurate mapping of short reads to reference sequences ".
BWA"BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp "
Bowtie"Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small"
VariationHunter"VariationHunter-CommonLaw is a tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies"
mrFASTIt is Micro Read Fast Alignment Search Tool. This tool is "designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner"
SOAP Aligner"It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer"
SOAPdenovo"SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads"
SOAPsnp"The program is a resequencing utility that can assemble consensus sequence for the genome of a newly sequenced individual based on the alignment of the raw sequencing reads on the known reference"
Celera Assembler/CABOGThis is "is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing"
BreakDancerBreakDancer-0.0.1 is a Perl package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads". It specifies the mapping quality threshold for ambiguous reads.
CNVnator"It is a tool for CNV discovery and genotyping from depth of read mapping". CNVnator 3.0 is the latest version avialable.
PEMer"PEMer package contains the computational codes and documentations for the algorithm developed to construct and analyze structural variants (SV)"
VarScanThis commandline based tool is used for "variant detection in massively parallel sequencing data".
Allpaths-LG"This blog provides the latest news concerning ALLPATHS-LG, the new short read genome assembler from the Computational Research and Development group at the Broad Institute"
VelvetIt is a "Sequence assembler for very short reads", maintained by EBI. "Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI)"
SSAHA2Sequence Search and Alignment by Hashing Algorithm (SSAHA2) "is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences". "SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package"
String Graph Assembler (SGA)"SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads"
IMPUTE2"IMPUTE version 2 is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009". "IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes."
GenSel SoftwareBIGS GenSel Login Page. GelSel is used primarily for statistical analyses associated with Genomic Selection. This software was developed by Dr. Dorian J. Garrick and Dr. Rohan Fernando at Iowa State University, USA.
AgBase v. 2.00"AgBase is a curated resource for functional analysis of agricultural plant and animal gene products including gene ontology annotations". It provides several functional analysis tools, including, GOProfiler, Genome2Seq, GORetriver etc.
Genome2Seq"Genome2Seq is used to rapidly retrieve a fasta file of sequences based on genome co-ordinates generated from RNA-Seq data".
gnuplot version 4.6"gnuplot is a command-driven interactive function plotting program. It can be used to plot functions and data points in both two- and three-dimensional plots in many different formats. It is designed primarily for the visual display of scientific data. gnuplot is copyrighted, but freely distributable".
SNPlotz: a genome plot tool for SNP association studies"SNPlotz is a web tool for users to plot phenotypic effects data from GWAS analysis, along a genome. The plot tool is coupled with the GBrowse to bring up all related genome features (transcripts, genes, QTL, etc) for further data mining on any interesting SNP shown on the plot".
Bioinformatics Services and Tools- CCMB, MI, USAUse this website to get guidelines on workflows of RNAseq, ChipSeq, Genome Assembly, Genome RNAseq and microarray analysis as well as list of several useful bioinformatics tools and resources.
Gene Ontology Tools"Gene Ontology (GO), the de facto standard in gene functionality description, is used widely in functional annotation and enrichment analysis".
MISO-The Sequence Ontology BrowserIts the "home page of the Sequence Ontology Project (SO), a joint effort by genome annotation centres, and other groups using sequence annotation data, including: WormBase, FlyBase, the Mouse Genome Informatics group, and the Sanger Institute". Aims at developing an ontology suitable for describing biological.
SNP NexusAn SNP annotation tool. "SNPnexus was designed to simplify and assist in the selection of functionally relevant Single Nucleotide Polymorphisms (SNP) for large-scale genotyping studies of multifactorial disorders".
Helix SystemThis system "evaluates new high performance architectures and introduces them into production work at NIH". Some of the function of this system are installing scientific application programs, evaluateing new high performance architectures, installing and supporting scientific application programs etc.
Samtools"SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments". "SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format".
Beagle v. 3.3.2"BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples". BEAGLE can be used for "phasing genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. infer sporadic missing genotype data", to "impute ungenotyped markers that have been genotyped in a reference panel", to "perform single marker and haplotypic association analysis" and to "detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals"
SniperIt is "a Bayesian probabilistic model that enables SNP discovery in both unique and repetitive regions of a genome by utilizing the information from multiply-mapped sequence reads"
GATK"The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance"
SEQanswers: Discussion ForumA discussion forum "intended to be oriented toward life sciences and next generation sequencing". However, "any scientific topic related to genomics is open for discussion".
Generic Model Organism DatabaseThe Generic Model Organism Database project is “a collection of open source software tools for creating and managing genome-scale biological databases”. It can be used “to create a small laboratory database of genome annotations, or a large web-accessible community database”.
Database management for SNP data (snpdb)"This project is used to facilitate the management and analysis of Single-Nucleotide Polymorphism (SNP) data from Genome-Wide Association Studies (GWAS) using a database system".
Myrna"Myrna is a cloud computing tool for calculating differential gene expression in large RNA-seq datasets. Myrna uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible"
Cufflinks"Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols"
Rnnotator"Rnnotator" software: To address challenges related to comprehensive annotation and quantification of transcriptomes, Rnnotator was developed by a team at the JGI to provide an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome"
Genomic Short-read Nucleotide Alignment Program (GSNAP)Used for aligning short reads of transcripts. It has added feature of enbling the user to check "for and eliminating indel/splice combinations at ends of alignments", "finding of microexons in short reads"
TopHat"TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons"
TrinityTrinity "represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads"
ERANGE"E-RANGE is our Python package for doing RNA-seq and ChIP-seq (hence the "dual-use"), and is a descendant of the ChIPSeq mini peak finder ". "ERANGE is not compatible with bowtie 0.9.9.X"
Trans-Abyss"Trans-ABySS is a software package that is designed to analyze ABySS-assembled whole-genome shotgun transcriptome data"
Scripture"Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio."
RUM"RUM is an RNA-Seq alignment pipeline"
G-Mo.R-SeG-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models. The "candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models"
MapSpliceIt is used for "accurate mapping of RNA-seq reads for splice junction discovery".
SpliceMap"SpliceMap is a de novo splice junction discovery and alignment tool. It offers high sensitivity and support for arbitrary RNA-seq read lengths"
OasesIt is used for "De novo transcriptome assembler for very short reads". "Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly"
SIFT"SIFT predicts whether an amino acid substitution affects protein function. SIFT prediction is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related sequences, collected through PSI-BLAST. SIFT can be applied to naturally occurring nonsynonymous polymorphisms or laboratory-induced missense mutations."
Polyphen-2"PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations".
snpEff v. 3.5"Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes)".
ANNOVAR"ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others)".
MEGAN4-MEtaGenome ANalyzerIt is a "stand-alone analysis tool for metagenomic of short-read data".
MG-RAST"MG-RAST (the Metagenomics RAST) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data". Its works the best in Firefox browser.
IMG/M“The Integrated Microbial Genomes (IMG) system serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. The IMG data warehouse integrates genome and metagenome datasets provided by IMG users with a comprehensive set of publicly available isolate and single cell genomes, and a rich set of publicly available metagenome samples”.
CAMERACAMERA (Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis) aims at serving the" needs of the microbial ecology research community, and other scientists using metagenomics data, by creating a rich, distinctive data repository and a bioinformatics tools resource that will address many of the unique challenges of metagenomic analysis".
CARMA"CARMA is a software pipeline for characterizing the taxonomic composition and genetic diversity of short-read metagenomes. The software was originally designed for the analysis of environmental metagenomes obtained by the ultra-fast 454 pyrosequencing system".
TerragenomeIts an international soil metagenome sequencing consortium.
QTL mapping softwareA QTL mapping software (in experimental crosses) in R environment.
Haploview“Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses, like, haplotype population frequency estimation, single SNP and haplotype association tests, permutation testing for association significance, implementation of Paul de Bakker's Tagger tag SNP selection algorithm” etc.
PyPop: Python for Population Genomics"PyPop (Python for Population Genomics) is an environment developed by the Thomson lab for doing large-scale population genetic analyses including: (1) conformity to Hardy-Weinberg expectations, (2) tests for balancing or directional selection; (3) estimates of haplotype frequencies (and their distributions) and measures and tests of significance for linkage disequilibrium (LD)".
Haplotype analysis (HapStat)"HAPSTAT is a user-friendly software interface for the statistical analysis of haplotype-disease association. HAPSTAT allows the user to estimate or test haplotype effects and haplotype-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty and study design".
Micro-Checker“Micro-Checker is a Windows application that checks for microsatellite null alleles and scoring errors. It also provides null allele estimates, and adjusts allele and genotypes frequencies”.
Microsatellite analyzer (MSA) 4.05“MSA is a universal, platform independent, data analysis tool”. It has been “designed to handle large microsatellite data sets”. “Microsatellite analyzer calculates the standard suit of descriptive statistics and provides input files for other software packages”.
MicrosatelliteMicro-Checker is a Windows application that checks for microsatellite null alleles and scoring errors. It also provides null allele estimates, and adjusts allele and genotypes frequencies.
Bayesian QTL mapping software for inbred linesContains link to Bayesian QTL mapping software.
Quantitative Trait Loci (QTL) Mapping SoftwareDiscussion and provision of links to some important QTL mapping software.
Molecular Genetics Software SuitesList of molecular genetic software (hyperlinked to the respective websites) pertaining to phylogenetics, primer deigning, population genetics, relatedness and parentage, restriction mapping etc., along with one line description.
HelixTreeGolden Helix is a commercial agency that provides several software for genetic-analysis and SNP analysis, DNAseq data analysis etc.
NTSYSpc, Numerical Taxonomy System, Version 2.2It is commercially available and is used to "discover pattern and structure in multivariate data". Thus it is helpful for clustering of data and dendogram construction (UPGMA based).
GenAlEX 6.5 SOFTWARE"GenAlEx 6.5 (Peakall and Smouse 2006, 2012) offers a wide range of population genetic analysis options for the full spectrum of genetic markers within the Microsoft Excel environment on both PC and Macintosh computers".
Real Time PCR Primer SetsThis site contains the validated primer-sets for real time PCR in human, mouse and other species for various chemistries used in quantitative PCR.
Human Mouse Homology RelationshipDisplays homology maps with reference to either human, or mouse or rat for "comparative mapping functions available in the Map Viewer".
GeneCards"GeneCards is a searchable, integrated, database of human genes that provides concise genomic related information, on all known and predicted human genes".
National Center for Genome ResourcesNCGR is US based non-profit organization that "offers Illumina® CSPro™ sequencing, analysis, assembly, annotation, genotyping and target enrichment services".
PopGenePopgene is "a user-friendly computer freeware for the analysis of genetic variation among and within populations using co-dominant and dominant markers", developed by "Francis Yeh, Rongcai Yang and Timothy Boyle".
LUCIA Cytogenetics site.It is the website of the image analysis software (developed by Laboratory Imaging s.r.o.) for the cytogenetics laboratories.
Cytogenetic ResourcesThe site contains links to cytogenetic software, tutorials, FISH, educational resources Idiograms for several species.
Arlequin 3.11Arlequin is "an Integrated Software for Population Genetics Data Analysis".
Bottleneck version 1.2.02"Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies".
Genepop 4.0.10"GENEPOP is a population genetics software package" originally developed by Michel Raymond and Francois Rousset.
PLINK"PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses (with genotype/phenotype data) in a computationally efficient manner".
Evo-TutorIt calculates and graphically displays various effects vis-à-vis amount of stochastic and deterministic factors as well as linkage equilibrium.
Statistical genetics software guideIt displays and introduces different online software on statistical genetics, viz. Genome Wide Association Programs, Haplotyping Programs, Linkage Analysis Programs, Pedigree Drawing Programs, Population Genetics Programs etc.
Genetic Statistics SoftwareThe web page of Juan Pedro Steibel (Michigan State University) provides three useful software, namely, QpowR, %QPCR_MIXED and LD Estimate.
Biostat software listA list of hyperlinked biostatistical software.
Statistics LinksAnother link to statistical software, mixture modelling, data fitting software, time series analysis, probability etc.
Genetic Analysis SoftwareAn exceptionally useful site enlisting the genetic software along with the relevant detail (full name, versions, description, authors, OS, website/ftp, source code etc). The software list has been arranged alphabatically.
Animal Genomics ResearchIt provides "links to Animal Genomics Research Web Sites and Database Resources".
National Assoc.of Anim. Breeders E GuideIt provides links to relevant sites that may be required by a breeder of domestic vis-à-vis pet animals.
Pedigree SoftwareA commercial agency (Tenset) that sells pedigree software like, Breeders Assistant, Pedserve, Pedigree Assistant.
Zooeasy Software"ZooEasy™ Software (commercial) offers a unique all-in-one solution for the (semi-) professional breeder of specific animal species".
ZooEasy Poultry SoftwareA commercial agency that develops and sells poultry breeding software for selection of breeding pairs, pedigree management, medical results recording etc.
Poultry Science Virtual LibraryIt is virtual library that contains links to several resources of information on poultry management, breeding, genetics, several corporations and industries.
Plant Breeding SoftwareThis site maintains plant breeding software, like, PLABSTAT, PLABQTL and PLABSTAT-PLABMQTL.
NEURONA software package for automated tuning of neuronal/network models
PyDSToolA Python tool for analysing dynamical systems in neuroscience
PyNNA simulator-independent language for building neuronal network models
STEPSSTEPS is a package for exact stochastic simulation of reaction- diffusion systems in arbitrarily complex 3D geometries, implementation of Gillespie's SSA, extended to deal with diffusion of molecules over the elements of a 3D tetrahedral mesh, studying any biochemical pathway, generating a mesh, controlling the simulation and generating and analysing output.
NeuroMacNeuroMac (Neuronal Morphologies and Circuits) is a computational framework to generate large amounts of virtual neuronal morphologies simultaneously, as well as their resultants microcircuits. For more information and downloads, please visit the NeuroMac page.
NeurofitterNEMO is a prototype implementation of a layer-oriented language for describing computational models of ion channels.
NEMONEMO is a prototype implementation of a layer-oriented language for describing computational models of ion channels.
CSPRCCSPRC is a MATLAB toolbox for estimating the infinitesimal phase response curve (PRC) by using Compressive Sensing (CS) algorithms.
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