Bioinformatics Softwares List
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- Category: Phylogenetic Analysis (continued)
- RFsupertrees 2.0 - Program for Constructing Accurate Supertrees
- RidgeRace - Ridge Regression for Continuous Ancestral Character Estimation on Phylogenetic Trees
- RIND 6.9.4 - Reconstructed Independence
- Rococo 2.0 - Reconstruct Ancestral Gene Clusters
- RootAnnotator 201402 - Computes Root Posterior Probabilities given a sample of Rooted Trees
- ROSE 1.3 - Random-model Of Sequence Evolution
- rRNA phylogeny - Phylogenetic Analysis (using Phylip) of rRNA
- rSPR 1.3.0 - Calculate Rooted Subtree-prune-and-regraft Distances and rooted agreement forest
- Saguaro 0.1 - Detect Signatures of Selection within Populations, Strains, or Species
- SATCHMO 2.06 / SATCHMO-JS - Simultaneous Alignment and Tree Construction using Hidden Markov Models
- SATé 2.2.7 - Simultaneous Alignment and Tree Estimation
- SATIVA 0.9 - Semi-Automatic Taxonomy Improvement and Validation Algorithm
- scaleboot 0.3-3 - Approximately Unbiased P-values via Multiscale Bootstrap
- SCI-PHY 3.01 - Subfamily Classification In PHYlogenomics
- ScripTree 17 - Scripting Phylogenetic Graphics
- SDBP 1.0 - Assessing Statistical Reliability of Phylogenetic Trees
- SDM - Fast Distance-based Approach for (Super)Tree Building in Phylogenomics
- Séance 0.11 - Reference-based Phylogenetic Analysis for 18S rRNA Studies
- SeaView 4.5.4 - Sequence Alignment and Phylogenetic Tree Building
- SEMPHY 2.0 b3 - Structural EM Phylogenetic Reconstruction
- SEPP - software for Phylogenetic Placement
- Seq-Gen 1.3.3 - Simulate the Evolution of Sequences along a Phylogeny
- seq-gen-cov - Modification of Seq-gen
- SeqQR 1.0.1 - Generate Nonredundant set of Protein Tree
- SGWE 7.3.5 / CoalEvol 7.3.5 - Simulation of Genome-Wide Evolution
- SHOT 2.0 - Shared Ortholog and Gene Order Tree Reconstruction Tool
- SICLE 1.0b - high-throughput tool for Extracting Evolutionary Relationships from Phylogenetic Trees
- Sifter-T 1.2.1 - Optimized Framework for SIFTER Phylogenomic method
- siMBa 1.0 - A simple GUI for MrBayes.
- SIMMAP 1.5.2 - StochastIc Mutational MApping on Phylogenies
- SimPhy 1.0.1 - A comprehensive Simulator of Gene Family Evolution
- simRRLs 1.5 - Simulate fastQ formatted RAD, ddRAD or GBS data on a fixed Species Tree
- SIMULATOR 1.0 - Simulate DNA and Protein datasets with well-defined Insertion-deletion dynamics
- Siphy 0.5 - SIte-specific PHYlogenetic analysis
- SISRS 1.6 - Site Identification from Short Read Sequences
- SISSI 1.0 - Simulating Sequence Evolution with Site-Specific Interactions
- SlidingBayes 0.94 - Exploring Recombination using a Sliding window approach based on Bayesian Phylogenetic inference
- SNPSTI - SNP Phylogeny Mapping tool
- SNSA - Construct Supernetwork from Partial Trees based on Simulated Annealing
- Softparsmap - Gene Tree Species Tree Reconicilation using Parsimony
- SPACoDi 0.1 / spacodiR 0.13.0115 - Structuring of Phylogenetic Diversity
- SPANNER 1.0.0 - Homology-based Taxonomic Classification of Protein Sequences
- Species Delimitation 1.03 - Geneious plugin for the exploration of Species Boundaries
- Spectrum 2.0 - Show Phylogenetic Information in a Data Set
- SPIDIR 0.9 - Species Informed Distance-based Reconstruction
- SPIMAP 1.1 - Species Informed Maximum A Posteriori Gene Tree Reconstruction
- SplitDist 1.1.7 - Calculate Number of Splits (edges) that Differs for two Trees
- SplitsTree 4.13.1 - Compute Phylogenetic Networks
- SPRDist 1.0.2 - computing Exact Subtree Prune and Regraft (SPR) Distance
- SPREAD 1.0.7rc - Spatial Phylogenetic Reconstruction of Evolutionary Dynamics
- SPRSupertrees 1.2.1 - Calculate Rooted Supertrees that Minimize the SPR Distance.
- SSA 1.0 - Inference of Maximum Likelihood Phylogenetic Trees Using a Stochastic Search Algorithm
- SSAMK - Inference of Maximum Likelihood Phylogenetic Trees for Morphological Data
- SSIMUL 1.2 - Speciation SIgnal extraction from MULtigene families
- stability - Stability Analysis of Phylogenetic Trees
- STAR-MP 1.0 - Species Tree informed Architecture Reconstruction - Maximum Parsimon
- Statio - Test Stationarity of Base Composition and Models
- STC 1.2 - Reconstruct Large Phylogenies
- STELLS 1.6.1 / STELLSH 1.0 - Inferring Species Tree from Gene Tree Topologies
- STEM 2.0 / STEM-hy 1.0 - Species Tree Estimation using Maximum likelihood (with hybridization)
- STS - Phylogenetic Inference program via Sequential Monte Carlo
- SuperFine - Supertree Estimation
- SuperQ 1.1 - Compute a Phylogenetic Super Network
- SuperTree 0.85b - Build Phylogenetic Supertrees
- SuperTriplets 1.1 - Triplet-based Supertree Approach to Phylogenomics
- SVD-Phy 1.0.0 - Phylogenetic profiling method based on SVD
- SylvX 1.3 - A Viewer for Phylogenetic Tree Reconciliations
- T-REX 4.01 - Reconstruct Phylogenetic Trees and Reticulation Networks
- TAGD - Phylogenetically Informative Substring Extraction
- TARGeT - Tree Analysis of Related Genes and Transposons
- TARGETING 1.0 - Solver for the Maximal Pairing Problem on Arbitrary Trees
- TargetOrtho - A Phylogenetic Footprinting Tool to Identify Transcription Factor Targets
- taxator-tk 1.3.0 - Taxonomic Sequence Assignment
- Taxy / Taxy-Pro - Fast Estimation of Metagenomic Taxon Abundances
- TCS 1.21 - Phylogenetic Network Estimation using Statistical Parsimony
- TERA 1.1 - Tree Estimating using Reconciliation and Amalgamation
- TESS 2.1.0 - Simulation of Reconstructed Phylogenetic Trees under Time-dependent Birth-death Processes
- TFBayes - Identification of Transcription Factor Binding Sites
- TIGER 1.02 - Identify Rapidly-evolving Characters in Evolutionary Data
- TIMER 0.1 - Estimate Divergence Times
- TimeTree 3.1 - Species Divergence Times on the Mobile Phone
- TipDate 1.2 - Estimate the rate of Molecular Evolution
- TIPP - Taxon Identification and Phylogenetic Profiling
- TIQ 1.0 - Browse Phylogenetic Trees of Toxins
- TMatch - compute Editing Distance of Two Ordered Trees
- TNT 201506 - Phylogenetic Analysis under Parsimony
- TOPD/FMTS 3.3 - Comparing Phylogenetic Trees
- TopiaryExplorer 1.0 - Interactive Phylogenetic Tree Viewing software
- TPMS - Tree Pattern Matching Suite
- tqDist 1.0 - a Triplet and Quartet Distance Library
- Tracer 1.6 - Analyse Results from Bayesian MCMC programs such as BEAST & MrBayes
- TransPhylo 1.0 - Inference of Pathogen Transmission Tree given Phylogeny
- TrAP - Tree Averaging program
- Tred – Draw Multi-page PDF Figures of Phylogenetic Trees
- Tree Tracker - Detecting Overrepresented Clusters in Hierarchical Tree
- tree-puzzle 5.2 - Maximum Likelihood Analysis
- TreeBeST 1.9.2 - Softwares for Phylogenetic Trees
- TreeChopper 20090606 - Cluster Tree Leaf Nodes According to Phylogenetic Distance
- TREECON 1.3b - Construction & Drawing of Evolutionary Trees
- TreeCorrect 1.2b - Compute Percentages of Tree Correct or Correct Tree
- TreeCounter - Compute the Number of possible Rooted and Unrooted Binary Trees
- TreeDyn 198.3 - Dynamic Graphics & Annotations for Phylogenetic Analyses
- TreeEdit 1.0a10 - Organize, View & Manipulate sets of Phylogenetic Trees
- TreeFam r9 - Database of Animal Gene Trees
- TREEFINDER 201103 - Computes Phylogenetic Trees from Molecular Sequences
- TreeFix 1.1.10 / TreeFix-DTL 1.0.2 - Statistically Informed Gene Tree Error Correction using Species Trees
- TreeGraph 2.4.0-456 beta - Graphical Editor for Phylogenetic Trees
- TreeJuxtaposer 2.1 - View a Single Tree, or Compare Two or more Trees
- TreeKO - Compare Phylogenetic Trees
- TreeLign 20100322 - Automatic update of 16s rRNA Phylogenetic Tree and Multiple Sequence Alignment in Metagenomics
- TreeMaker 1.3 - Interactive Building of Taxonomies
- TreeMap 3.0b - Compare Host & Parasite Trees
- TreeMe 200807 - Visualization, Editing and Annotation of Phylogenetic Trees
- TreePar 3.3 - Estimating Birth and Death Rates based on Phylogenies
- Treephyler 1.1 - Fast Taxonomic Profiling of Metagenomes.
- TreeSAAP 3.2 - Selection of Amino Acid Properties using Phylogenetic Trees model
- TreeSample 1.0 - Algorithms for Sampling Evolutionary Models of Speciation
- TreeScan 1.0 - Genotype-phenotype Associations from Haplotype Trees
- TreeSim 2.1 / TreeSimGM 1.2 - Simulating Trees under the Birth-Death Model / under a General Model
- TreeSnatcher Plus 201206 - Phylogenetic Tree Capturing Tool
- TreeStat 1.2 - Calculate Summary Statistics of a set of Trees
- TreeTest - Testing Phylogenetic Tree Topologies in a Frequentist Framework
- TreeTime 1.0.1 - Bayesian Sampling of Phylogenetic Trees from Molecular data
- TreeView 1.6.6 / TreeView X 0.5-1 - Tree Drawing Software
- TreeViewJ 1.1.2 - View & Analyze Phylogenetic Trees
- TreeViewX 0.5.1 - Program to Display Phylogenetic Trees
- TreeVis - A MATLAB-based tool for Tree Visualization
- Treevolution 1.2 - Visual Analysis of Phylogenetic Trees
- TreSpEx 1.1 - Detection of Misleading Signal in Phylogenetic Reconstructions
- TriLoNet 1.0 - Construct Rooted Level-1 Phylogenetic Networks
- TripleC - Constuct Consensus Trees from Rooted Triples
- TripNet - Constructing Phylogenetic Networks from Sparse Sets of Rooted Triplets
- TVi 1.01 - Tree Viewer with Interactions
- TWARIT - Phylogenetic Classification of Metagenomic Sequences
- txgen 0.1 - PAUP Text Generator and Parser
- Ultranet - New Tool For Phylogenetic Analysis
- UltraNet 20150606 - UltraFast Tool for Minimum Reticulate Networks
- UnderlyingApproach - Alignment-Free Phylogeny of Whole Genomes using Underlying Subwords
- Unrooted - Draw Binary Tree Expressed in the standard Phylogenetic Tree Format
- UpdownDistance - Tool for comparing phylogenetic trees
- UREC 1.02 - Unrooted REConciliation
- urRF - unrooted Gene Trees vs rooted Species Trees
- Vanilla 1.2 - Programs to Access Features in PAL
- Vestige - Maximum Likelihood based Phylogenetic Footprinting Application
- Vim Nexus syntax highlighting - Nexus syntax highlighting files for the Vim editor
- VIP 20110914 - Historical Biogeography Analysis
- ViralNet - Computing Network Structures in RNA Viral Populations
- VisRD 3.0 - Visual Recombination Detection Software package
- Vizardous 1.2.0 - Analysis of Microbial Populations with Single Cell Resolution
- VTC - A simple Visual Tree Comparison Tool
- Weighbor 1.2 - Weighted Neighbor Joining
- windex 1.0 - Analysing Convergent Evolution using the Wheatsheaf index
- WinIPaup 1.0 - Windows Interface for PAUP to Create NEXUS Files
- Wombac 2.0 - Bacterial core Genome SNPs for Phylogenomic Trees from NGS Reads and/or draft genomes
- XplorSeq 2.0.7 - Management of Nucleic Acid Sequences for Phylogenetic Analysis
- Xscape - Tools for Maximum-Parsimony Phylogenetic Tree Reconciliation over the Event Cost Landscape
- YTool 1.0 - Retrieving Y Chromosomal Haplogroup Trees
- πBUSS 1.3.8 - BEAST/BEAGLE utility for Sequence Simulation
- Category: Plasmid / Chemical Drawing
- ACD/ChemSketch 2015 - Draw Chemical Structures
- ApE 2.0.49 - A Plasmid Editor
- BIOVIA Draw 4.2 - Chemical Structure Drawing Tool
- BKChem 0.14.0-pre2 - Free Chemical Drawing Program
- BVTech Plasmid 5.1 - DNA Sequence Analysis & Plasmid Drawing Software
- CGView 1.0 - Generat Maps of Circular Genomes
- Chem4Word 2.0.1.0 beta5 - Chemistry Add-in for Word
- ChemDoodle 7.0.2 / ChemDoodle Mobile 1.5.0 - Chemical Drawing Application
- ChemDraw Ultra / ChemDraw ActiveX/Plugin Viewer 15.0 / ChemDraw for iPad 2.0.1 - Draw / View Chemical Structures
- ChemFormatter 2.0.0 - Chemical Font Add-in for Microsoft Office
- ChemicPen 2.6 - Draw 2D Chemical Formulae & Reactions
- Chemistry 4-D Draw 8.0.2 - Chemical Structure Drawing
- Gene Construction Kit 4.0.3 - Plasmid Mapping, DNA Cloning Analysis, Vector Manipulation
- GenomeVx 20130228 - Creation of editable Circular Chromosome Maps
- Graphviz 2.38 + SBOLv 1.0 - Easy Drawing of promoter->gene->terminator Diagrams
- JChem for Office 15.6.1500 - Chemical Structure Handling & Visualizing within Microsoft Office
- JChemPaint 3.3-1210 - Editor for 2D Molecular Structures
- jlogP 2.3 - Calculates Hydrophobicity & Molecular Formula of Molecules
- JME 2010.02 / JSME 20150614 - Java Molecular Editor
- JMolDraw 0.6 Alpha - 2D Chemical Structure Drawing Program
- KegDraw 0.1.14 beta - Draw Compound & Glycan Structures
- Marvin 16.5.2.0 - Draw & Visualize Chemistry
- MCDL 20070701 - Java Molecular Viewer/Editor for Chemical Structures
- MOLGEN 5.0 - Molecular Structure Generation
- MolPrime 1.0.6 - Chemical Structure Drawing Tool for Android
- NoeClone 3.0 - Molecular Cloning Tool
- OGdraw 1.1.1 - Generate high-quality Graphical Maps of circular DNA Sequences
- pDRAW32 1.1.130 - DNA Analysis Software
- PlasmaDNA 1.4.2 - PLAsmid MAnipulation program
- PlasMapper 2.0 - Web Server for Drawing & Auto-annotating Plasmid Maps
- Plasmidomics 0.2 - Plasmid Drawing Program
- pLOT 1.0.10h - Plasmid Mapping Freeware
- PLT 7.1.19 - Draw Chemical Structures
- PoseView 1.1.2 - Creates Two-dimensional Diagrams of Complexes with known Complex Structure
- savvy 0.1 - Generate High Resolution Print Quality Plasmid Map
- SimVector 4.60 - Draw Vector Maps
- SnapGene Viewer 3.1.2 - Create, Browse, and Share richly Annotated DNA Sequence
- WebChem Viewer 1.2.7 - Sharing Molecular Structures and Associated Chemical Information
- WebDSV - Free Online DNA Sequence Editor and Plasmid Drawing program
- WinDrawChem 1.6.2 - Molecule Structure Drawing
- XDrawChem 1.9.9 - Molecule Structure Drawing
- XPlasMap 0.99 - DNA Mapping Program
- Zem 0.3 - 2D Molecular Editor
- Category: Protein Sequence Analysis
- (PS)2 v3 - Protein Structure Prediction server
- 14-3-3-Pred - Webserver to predict 14-3-3-binding sites in Proteins
- 1D - Protein Structure Prediction Server
- 2D-MH - Generating Graphic Representation of Protein Sequences
- 2ZIP - Prediction of Leucine Zipper Domain from the Protein Sequence
- 3D-BLAST beta 1.02 - Protein Structure Search
- 3D-partner - Infer Interacting Partners and Binding Models
- 3D-SURFER 2.0 - Real-time Search and Characterization of Protein Surfaces
- 3DRobot 1.0 - Protein Structural Decoy Generator
- 3MATRIX 1.0 - Motif in 3D
- 3MOTIF 2.0 - Motif in 3D
- AAIndexLoc - Predicting Protein Subcellular Localization Using Amino Acid Index
- ABAG - Computation of Antibody/Antigen Concentration and Endpoint Titer
- AbAmyloid 1.0 - Prediction of Antibody Amyloidogenesis from Sequences
- ABangle - VH-VL Orientation Analysis
- ABCpred - Artificial Neural Network based B-cell Epitope Prediction Server
- AbDesigner - Design of Peptide-directed Antibodies
- acACS 1.0 - Auto Covariance of Average Chemical Shifts
- AcalPred - Discriminating Acidic Enzymes from Alkaline Enzymes
- aCSM - atomic Cutoff Scanning Matrix
- AdaPatch 1.0 - Searche for Dense and Spatially Distinct Clusters of sites
- ADDA version 4 - Automatic Domain Decomposition Algorithm
- AFPredictor - Predicts potential Ice-binding Sites based on Geometric Analysis of the Protein Surface
- AGGRESCAN - Prediction and Evaluation of "hot spots" of Aggregation in Polypeptides
- Agos - GW Argonaute-binding Domain Prediction
- AIS - Classify Amino Acids
- Algpred - Prediction of Allergenic Proteins and mapping of IgE Epitopes
- Allerdictor - Fast Allergen Prediction using Text Classification with SVM
- AllergenFP 1.0 - Allergenicity Prediction based on a novel descriptor Fingerprint Approach
- AllerTOP 2 - Allergenicity Prediction
- Allosite 2.0 - Prediction of Allosteric Sites in Protein
- Alphabet - Find Groups of Amino Acids that Co-occur in Columns Frequently
- AlphaPred - Prediction of Alpha-turns in Proteins using Multiple Alignment and Secondary Structure Information
- Ampred - Predict the Antimicrobial Activity of given Sequence
- AMS 4.0-1.5 - Consensus Prediction of Post-translational Modifications in Protein Sequences
- AmyloidMutants - Probing the Mutational Landscape of Amyloid Structure
- AMYLPRED - A Consensus Method for Amyloid Propensity Prediction
- AnaGram - Protein Function Prediction
- ANARCI - Antigen Receptor Numbering And Receptor ClassificatIon
- Anchor - Predict Binding Regions in Proteins
- AnDom - Assign Structual Domains to Protein Sequences
- ANGLOR - Backbone Torsion Angle Predictor
- ANNIE - Protein Sequence Annotation and Interpretation Environment
- ANTHEPROT 6.3.1 - Protein Sequence Analysis
- AntiAngioPred - Prediction of Anti-Angiogenic Peptides
- AntiBP - Prediction of the Antibacterial Peptides
- AntiCP - Prediction and Designing of Anticancer Peptides
- AodPred - Identifying Antioxidant Proteins by using optimal Dipeptide Compositions
- APAT 1.4.1 - Automated Protein Annotation Tool
- APCpred - B Cell Linear Epitope Prediction
- APOLLO - Assess Protein Single or Multiple Model(s)
- APSSP2 - Advanced Protein Secondary Structure Prediction Server
- Ar_NHPred - Prediction of Aromatic Backbone NH Interaction in Proteins
- ArchCandy 1.0 - Detect Regions in Protein Sequences that have a potential to form Amyloids
- ArchKI - Classification of common Functional Loops of Kinase Super-families
- ArchPred - Knwoledge-based Loop Structure Prediction method
- ArchSchema 1.1 - Generate Dynamic Plots of related Pfam Domain Architectures
- ARD2 - Alpha-rod Detector
- AS-EAST 1.1.1 - Annotate and Analyzes users' uploaded Transcript data
- ASAView - Solvent Accessibility Graphics for Proteins
- ASD - Measuring Global Shape Divergence of Protein Fragments
- ASEB 1.15.0 - A Web Server for KAT-specific Acetylation Site Prediction
- ASSAM / SPRITE - Side Chain 3D-motif Searching in Protein Structures
- ASSIST v1- Active Site Similarity Search Tool
- ASSP 1.0 - Analysis of Secondary Structure Elements in Proteins
- assp 1.2 - Assess Protein Secondary Structure Prediction Accuracy
- Asymmetry 20060215 - Test Protein Sequence data for Substitutional Asymmetry
- ATPint - Prediction of ATP interacting protein residues
- AtSubP - Arabidopsis Subcellular Localization Prediction Server
- B-Pred - Structure based B-cell Epitopes Prediction Server
- BaCelLo - Predictor for the Subcellular Localization of Proteins in Eukaryotes
- BAR+ - Functional and Structural Annotation of Protein sequences
- BayesMotif 1.0 - Sorting Motif Discovery using Bayes Classifiers
- BcePred - Predict B cell Epitope based on Physio-chemical Properties of Amino Acids
- BCL 3.2.1 - Protein Structure Determination from sparse Experimental data
- BCov 1.0 - Predicting Protein beta-sheets from Sequence
- BEAN 1.0 - Bacteria Effector ANalyzer
- BeAtMuSiC 1.0 - Prediction of Binding Affinity Changes upon Mutations
- BepiPred 1.0b - Linear B-cell epitopes
- BETApro 1.0 - Protein Beta Sheet Predictor
- Betascan 20081027 - Predict Beta-sheets from Sequence alone using Pairwise Probabilistic Modeling
- BetaTPred - Predict Beta Turns in Proteins using Existing Statistical methods
- BetaTPred2: Prediction of Beta-turns in Proteins using Neural Networks and Multiple Alignment
- Betaturns - Prediction of Beta-turn Types
- BetAware - Beta-Barrel Detection and Topology Prediction
- BetaWrap / BetaWrapPro - Scores Sequences for Compatibility with the Right-handed beta-helix Fold
- BHAGEERATH-H / Bhageerath 1.0 - Energy Based Protein Structure Prediction
- BhairPred - Prediction of beta Hairpins in Proteins using ANN and SVM Techniques
- BiasViz 2 - Protein Amino Acid Bias Analysis Applet
- BindUP 1.0 - Predicting DNA and RNA Binding Proteins using Electrostatic Patches
- BinMemPredict - Predicting Membrane Protein Types
- BioAssemblyModeler (BAM) 2.0.14.0 - Homology Modeling of Protein Homo- and Heterooligomers
- BION - Predicting Non-specifically Bound Surface Ions
- BiopLib 3.4 / BiopTools 1.2 - C Programming Library and Toolset for Manipulating Protein Structure.
- BIS - Analysis of the Coevolution of Amino-acid Fragments in Proteins
- BJTEpitope - T-cell Epitope Prediction for the MHC class I allele HLA-A*0201
- BLANNOTATOR - Homology-based Function Prediction of Bacterial Protein
- BLinks 2.0 - Software for PIR Technology
- Bluues 2.0 - Electrostatic properties of Proteins based on generalized Born radii
- BND - Improving accuracy of Protein Contact prediction using Balanced Network Deconvolution
- BOCTOPUS 2.0 - Topology Predictor for Beta-barrel Membrane Proteins
- BOMP - The beta-barrel Outer Membrane Protein Predictor
- BPBAac - T3S effector prediction tool based on position-specific Amino Acid composition features in N-termini
- bPE toolkit – Basic Protein Engineering Toolkit
- BRS-nonint - Balanced Random Sampling of Non-interactions between Proteins
- BsFinder - Predicting the Binding Sites for the Given Proteins
- BSpred - Predict Binding Site of Proteins
- BTEVAL - Evaluation of beta-turn Prediction
- BTXpred - Prediction of Bacterial Toxins
- C-HMM 1.0 - Program to Identify Remote Homologues from Protein Sequence Database
- CaLecPred - A Sequence-based Predictor for Identifying Cancerlectin
- CalPred 1.0 - Calcium Binding Protein Predictor
- CamSol - Rational Design of Protein Mutants with enhanced Solubility
- CanBind - Exploring Protein Binding sites Mutated in Cancer
- CancerPred - Prediction of Cancer Lectins
- CanPredict - Computational tool for Predicting Cancer-associated Mutations
- CAPS 1.0 - Coevolution Analysis using Protein Sequences
- Carboxylator - Classification of Transporters using Efficient RBF Networks
- CarSPred 1.0 - Predicting Carbonylation Sites of Human Proteins
- Cascleave 2.0 - Caspase Substrate Cleavage Site Prediction
- CASS 1.1 - Coarse-grained Artificial Sequence Simulator
- CAST 1.0 - Compositional Bias Detection Algorithm
- catRAPID - Prediction of Protein-RNA Interactions
- catRAPID signature - Identification of Ribonucleoproteins and RNA-Binding Regions
- CBS-Pred - Prediction of Carbohydrate-binding sites from Sequence and PSSM
- cbsPredict - Detect Potential Carbohydrate-binding Sites in Protein 3D Structures
- CBTOPE - Conformational B-cell Epitope Prediction
- CCCP - Coiled-coil Crick Parameterization
- CCCPP - Compute Cavites, Channels, Pores and Pockets in Proteins
- CCHMM - Predictor of Coiled-Coils Regions in Proteins
- CCHMMPROF - Predictor of Coiled-Coils Regions in Proteins Exploiting Evolutionary Information
- CCMpred 0.3.1 - Prediction of Protein Residue-residue Contacts from Correlated Mutations
- CCRXP - Identifies Clusters of Conserved Residues in Proteins using PDB files
- CCSOL / ccSol omics - Prediction of Protein Solubility
- CCTOP 1.00 - Constrained Consensus TOPology prediction server
- cdBEST - Chromatin Domain Boundary Element Search Tool
- CDPred 1.01 - Conserved Domain-based Prediction
- CDvist - Comprehensive Domain Visualization Tool
- Cell-PLoc 2.0 - Predicting Subcellular localization of Proteins in different Organisms
- CELLO v.2.5 / CELLO2GO - subCELlular LOcalization predictor
- CellPPD - Designing of Cell Penetrating Peptides
- CFP - Constructing Sequence-based Protein Conformational Flexibility Profiles
- CGAP - Contact Geometry Analysis Plugin for CMView
- ChainTweak - Sampling from the Neighbourhood of a Protein Conformation
- Change-O 0.3.2 - Analyzing Immunoglobulin Sequences
- ChIPCor 1.1.0 - Measuring the Spatial Correlations of Protein Binding Sites
- Chiron - Protein Energy Minimization server
- ChloPred - Prediction of Subchloroplast Locations of Proteins
- ChloroP 1.1 - Predict Chloroplast Transit Peptides
- CHpredict - Predict C-H...O and C-H...PI Interactions
- CISRR 1.02 - Prediction of Side-chain Modeling
- CKSAAP_OGlySite - Predictor of Mucin-type O-glycosylation Sites
- CKSAAP_UbSite / hCKSAAP_UbSite - A Predictor of Protein Ubiquitination sites
- CKSAAP-Palm 20100528 - Predict Palmitoylation Sites from Protein Sequences
- CLANS 20101007 - Visualize Protein Families based on Pairwise Similarity
- ClanTox - A Classifier of Animal Toxins
- CLEVER 1.0 - Sequence based Approximation of Protein Energies
- cleverSuite - Protein Characterization
- CLIPS-1D / CLIPS-4D - Predicting Functionally and Structurally Important Residue-positions based on 1D / and 3D data
- Cloud4Psi - Protein 3D Structure Similarity Searching in Microsoft Windows Azure cloud
- ClusCo 0.3 - Clustering and Comparison of Protein Models
- CMAT 0.3.2 - Correlated Mutation Analysis Tool
- co-evo - Correlated Evolutions of Transcript Factors and their Binding Sites
- CoBaltDB 1.0 - Complete Bacterial and Archaeal Orfeomes Subcellular Localization Database
- Codep 1.0 - Maximizing Co-evolutionary interdependencies to Discover Interacting Proteins
- Coevolution - Coevolution Analysis of Protein Residues
- COFACTOR - Structure-based Protein Function Annotation
- Cofactory v.1.0 - Identification of Rossmann folds and prediction of FAD, NAD and NADP specificity
- COILS 2.2 - Prediction of Coiled Coil Regions in Proteins
- CoinFold - Protein Contact Prediction and Contact-assisted Protein Folding
- CombFunc - Protein Function Prediction Server
- CoMPAS 20070115 - Comprehensive Meta Prediction and Annotation Services for Proteins
- ComplexCorr - Predict the Connectivity of Subunits within large Protein Complexes
- Composition Profiler 1.1 - Discovery of Amino Acid Composition Differences
- COMSAT - Residue Contact Prediction for Transmembrane Proteins
- COMSPA - Predicting Protein Structural Classes from Primary Sequence
- ConDens - Predict Kinase Substrates using Conservation of Local Motif Density
- ConPlex - Evolutionary Analysis of Protein Complex Structure
- ConQuass - Quality Assessment of Protein Model-Structures using Evolutionary Conservation
- conSSert - Consensus Secondary Structure Prediction
- ConSurf 2010 - Identification of Functional Regions in Proteins
- Contact-based Domain Predictors - Prediction of Protein Domain Boundaries From Inverse Covariances
- ConTest 1.0.2 - Test Constraints in Proteins
- ContextShapes - Protein Docking and Partial Shape Matching
- COPid - Composition Based Comprehensive Tool
- COPRED - Prediction of Fold, GO Molecular Function and Functional Residues at the Domain Level
- CorMut 1.10.0 - Detect the Correlated Mutations based on Selection Pressure
- CORNET - Predictor of Residue Contacts in Proteins
- COTH - Co-Threading of Protein-Protein Complex Structures
- COUDES - Prediction of Beta-turns and their Types
- CPLA 1.0 - Integrated Database of Protein Lysine Acetylation
- CPred - Predicting Viable Circular Permutations in Proteins
- CPSP Tools 2.4.6 - Constraint-based Protein Structure Prediction
- CRC64 2006 - Improved 64-bit Cyclic Redundancy Check for Protein Sequences
- CreateEpitome 1.0.0.1 - Take amino acid sequences and Create Epitomes
- Crescendo - Identifying Functional Sites in Proteins
- CRNPRED 1.1 - Predict Secondary Structures of Protein
- CRUSH - CoReceptor USage prediction for HIV-1
- Crysalis - Computational Analysis and Design of Protein Crystallization
- CRYSTALP2 - Sequence-based Protein Crystallization Propensity prediction
- CS-PSeq-Gen 1.0 - Simulation of Protein Sequences under Constraints
- CSM - Funciton Prediction and Fold Recognition by Protein inter-residue Distance Patterns
- csnpAnalysis 1.03 - PANTHER Coding SNP Analysis tool
- CSpritz 1.2 - Prediction of Protein Disorder with 3 Separate Predictors
- CSS-Palm 4.0 - Palmitoylation Site Prediction with a Clustering and Scoring Strategy
- CTLPred - SVM & ANN Based CTL epitope Prediction method
- Cubic 2.0.4 / JCubic 1.1 - Protein Binding Site Prediction
- CUPSAT - Protein Stability Analysis Tool
- CycloPs 1.32 - Generates Cyclic Peptides
- Cycloquest 20110907 - Identification of Cyclopeptides via Database Search
- CyPred - High-throughput Prediction of Cyclic Proteins
- Cyscon 20150118 - Disulfide Connectivity Prediction Server
- CytoPre - Cytokine Prediction System
- d-Omix - Mixer of Protein Domain Analysis Tools
- DAMA - Protein Domain Architectures
- DAPPLE 2 - Homology-based Prediction of Phosphorylation Sites
- DAS-TMfilter - On filtering False Positive Transmembrane Protein Prediction
- DASher 1.3.4 - Protein Sequence Client for DAS
- dasty 3.0.0.9 - Visualize Protein Sequence Feature Information using DAS
- DBD2BS - Connecting a DNA-binding Protein with its Binding Sites
- DBindR - Prediction of DNA-binding Residues in Proteins
- dbPTM 3.0 - Information Repository of Protein Post-translational Modification
- DBS-PRED - Prediction of DNA-binding in proteins using Neural Networks
- DBS-PSSM v3 - Predicts DNA-binding sites in Proteins
- DBToolkit 4.2.3 - Manipulating fasta Sequence Databases
- DCF 0.6 - Peptide Design by Compatible Functions
- DCON - Predictor of Disulfide Connectivity in Proteins
- dDFIRE 1.1 / DFIRE 2 - Monomer Protein Energy Calculation
- DDNA 3.1 - DNA/Protein Complex Interaction Energy
- DECOMP - PDB Decomposition Tool
- deconSTRUCT - Protein Structure Comparison and Database Search
- DelPhi - Poisson-Boltzmann solver for calculating Electrostatic Energies and potential in biological macromolecules
- DEME 1.0 - Motif Discovery using Positive & Negative Examples
- DeNovo Pipeline 1.5 - Protein Identification by de novo Interpretation
- Dependency 2.1 - Detect Functional Interactions between Amino Acids in Proteins
- DephosSite - Discovering Phosphotase-specific Dephosphorylation Sites
- DEPTH 2.8.7 - Measure Extent of Atom/Residue Burial within Protein
- DescFold - Descriptor-based Fold Recognition System
- DiANNA 1.1 - Cysteine state and Disulfide Bond partner prediction
- DICROPROT 2000 - DICHROism of PROTeins
- DILIMOT - Discovery of Linear Motifs in Proteins
- DIpro 2.0 - Protein Disulfide Bond Prediction
- DISCERN - Catalytic Residue Prediction
- DISCO 1.0 - Structure Determination of Protein Homo-oligomers
- DisCon - Disorder Content Prediction
- DisCons - Quantify and Classify Evolutionary Conservation of Intrinsic Protein Disorder
- disCoP - Disorder Consensus-based Predictor
- DiscoTope 2.0 - Predicts Discontinuous B cell Epitope
- Discriminative HMMs - Find Discriminative Motif to Predict Protein Subcellular Localization
- DisEMBL 1.5 - Protein Disorder Prediction
- DisLocate - Find Disulfide bonds in Eukaryotes with predicted subcellular Localization
- DISOPRED 3.16 - Intrinsic Protein Disorder Prediction
- DisoRDPbind - Prediction of RNA, DNA and Protein Binding Regions
- DisPhos 1.3 - Disorder-Enhanced Phosphorylation Sites Predictor
- DisplayFam 1999 - Protein Familly Viewer
- DisPredict 1.0 - Disorder Protein Predictor
- DISpro 1.0 - Prediction of Disordered Regions from Protein Sequences
- Distill 2.0 - Prediction of Structural Features of Proteins
- DLocalMotif - Discover Local Motifs in Protein Sequences
- DN-Fold - Protein Fold Recognition System using Deep Learning Networks
- DNAbind - DNA Binding Protein prediction
- DNABind - DNA Binding Residue Prediction
- DNAbinder - Prediction of DNA-binding Proteins
- DNABindProt - Server for Determination of Potential DNA Binding Sites of Proteins
- DNABR - Prediction of DNA-binding Residues
- DNdisorder - Predicting Protein Disorder using Boosting and Deep Networks
- DoBi 1.5 - Predicting the Binding Sites on pair of given Proteins
- DoBo - Protein Domain Boundary Prediction by integrating Evolutionary Signals and Machine Learning
- DockRank 20140320 - Rank Docked Models Using Predicted Partner-Specific Protein-Protein Binding Sites
- Domain Fishing 1.0 - Look for Recognizable Protein Domains
- DomainFinder 2.0.4 - Determine Dynamical Domains in Protein
- DomainParser 2 - Protein Structure Domain Partition
- DomEx - Extending Protein Domain Boundary Predictors
- DOMIRE - DOMain Identification from Recurrence
- DoMo-Pred - Domain-Motif Mediated Interaction Prediction
- DoMosaics 0.95 - Domain-centric Analysis of Proteins
- DOMpro 1.0 - Protein Domain Prediction
- doublet 1.0 - Incorporate Patterns of Dipeptide Covariation to Align Protein Sequences
- Dover Analyzer 0.1.2 - Overlap and Diversity in Antimicrobial Peptide Database
- dPABBs - Predicting and Designing Anti-biofilm Peptides
- DPD - Identification and Quantification of the Protein
- DPROT - Prediction of Disordered Proteins
- DPUC 2.0 - Using Context to Improve Protein Domain Identification
- DrawCoil 1.0 – Produce Coiled-coil Helical Wheel Diagrams
- DSPMP - Discriminating Secretory Proteins of Malaria Parasite
- DSSP 2.2.1 - Calculates DSSP Entries from PDB Entries
- DUET - Predicting Effects of Mutations on Protein Stability
- DynaFace - Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions
- DynaMine Beta - Predicting Protein Dynamics from Sequence
- e-Driver - Identify Protein Regions driving Cancer
- EagleEye 1.66 - Remove Background MS/MS Spectra
- eBLOCKS - Database of Conserved Protein Regions
- EFC-FCBF - Framework for Feature Construction and Selection for Improved Recognition of Antimicrobial Peptides
- EFI-EST - Generating Protein Sequence Similarity Networks
- EFICAz 2.5 - Accurate Sequence based Approach to Enzyme Function Inference
- EFIN - Evaluation of Functional Impact of Nonsynonymous SNPs
- ELASPIC - Ensemble Learning Approach for Stability Prediction of Interface and Core Mutations
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