Posts
- Category: 3D molecular model (continued)
- RDCvis 1.02 - Residual Dipolar Coupling Visualizer
- Reconstruct 1.0 - Reconstructing 3D Structures from Contact Maps
- RedMD 2.3 - Perform Molecular Dynamics Simulations for Coarse-grained Models
- Reduce 3.23 - Add Hydrogens to PDB Molecular Structure File
- Remediator 1.60 - Convert PDB Files between PDBv2.3 & PDBv3.2 Formats
- REMO 2.0 - Construct Full-atom Protein Models from C-alpha Traces
- Repertoire Builder - High-throughput structural modeling for B-cell and T-cell receptors
- Reveal - Viewer for Automated active-site Predictions for Polypeptides
- Ringer - Detect Molecular Motions by automatic Electron Density Sampling
- RIP 1.1 - Accelerated Molecular Dynamics
- RNA2D3D 5.7.0 - Conversion of RNA 2D Structures to 3D and 3D Modeling
- RNABC 1.11 - RNA Backbone Correction
- Rosetta@home 3.65 - Grid Software for Protein Folding
- RPISeq - RNA-Protein Interaction Prediction
- SAVR 20050411 - Semi-Automated Virus Reconstruction
- SAXSTER - SAXS-assisted Protein Fold Recognition
- SCL 1.0 - Three-dimensional Chromosome Structures from Single-cell Hi-C data
- ScoreDotsAtAtom 1.0 - Bookkeep All-atom Contact Dot
- Sculptor 2.1.1 - Docking & Visualization for Atomic Structures
- SDA 7.2.3 / webSDA 1.0 - Simulation of Diffusional Association
- SEED 4.0.0 - Solvation Energy for Exhaustive Docking
- SelfAT-Fold - Protein Fold Recognition
- SEMBA - Single-rEsidue Mutational based Binding Affinity
- SEQMOL 3.4.7 - Sequence Alignment & PDB Structure Analysis Utility
- sequins 20070909 - Validation of Sequence Assignment
- ShaEP 1.3.0 - Align Two Rigid 3D Molecular Structure Models
- SheeP 1603061903 - Description of β-sheets in Protein 3D structures
- Shiftcor 1.3 - Compares, Identifies, Corrects and Re-referencs Protein Chemical Shifts
- SHIFTOR - Predicting Torsion Angles in Proteins from NMR Chemical Shifts and Sequence Homology
- SHIFTS 5.5 - Predict Nitrogen, Carbon & Proton Chemical Shifts in Proteins
- SHIFTX2 1.13 - Improved Protein Chemical Shift Prediction
- SIfTER 2015 - Mapping Protein Conformation Spaces
- SimTK Core 2.1 - Simbios Biosimulation ToolKit
- SIRAH 2.2 - Mapping, Backmapping and Visualization of Coarse-grained Models
- Situs 3.1r2 - Integration of Multi-Resolution Structures
- SketchBio 0.0.10 - 3D Interface for Molecular Modeling and Animation
- SLITHER - Prediction of free Energy Profile along the Access Channel within a Protein
- SMOG 2.4.2 / OpenSMOG 1.1 - Structure-based Models for Biomolecules
- SnB 2.3 - Determine Crystal Structures from X-ray Diffraction Data
- SOESA 0.21b - Structure Optimization and Evaluation using Separations of Atoms
- SolubiS 1.0 - Optimize your protein
- Solvate 1.0 - Construct Atomic Solvent Environment Model for Given Atomic Macromolecule Model
- SOLVE / RESOLVE 2.13 - Automated Crystallographic Structure Solution for MIR, SAD, and MAD
- SPADE 1.3 - Structural Proteomics Application Development Environment
- Spanner - Hybrid-template Structural Modeling
- SpotOn - Determination of Hot-Spots at Protein-protein interfaces
- SRS3D 1.4 - System for Displaying 3D Structures integrated with Sequences and Features
- StarBiochem 2.3 - 3D Protein Viewer
- STOVCA 3.95 - Comparison, Ranking and Evaluation of Structure Alignments
- StrukEd - Editor for Molecules & 3D Viewer
- STRuster 3.1 - Comparison and Analysis of Alternative Structural Models
- Suitename 0.3 - RNA Conformer
- SuMo 5.0 - 3D search for Functional Sites
- Superficial 1.2 - Identification of Potential Epitopes or Binding Sites
- SuperMimic - Fit Peptide Mimetics into Protein Structures
- SuperPose 1.0 - Sophisticated Structural Superposition
- SURFace - Calculate Solvent accessible surface area
- Surface Diver - Comparing, and Classifying Proteins according to their Physicochemical Properties
- Surface Racer 5.0 - Calculation of Accessible and Molecular Surface Areas and Average Surface Curvature
- SURFNET 1.5 - Visualize Molecular Surfaces, Cavities, Density Distributions and Sidechain Interactions
- SVMcon 1.0 - Protein Contact Map Prediction using Support Vector Machine
- SwarmDock - Webservice for Generating 3D Structures of Protein-protein complexes
- SweetMollyGrace 1.3 - Rendering and Animating Molecules
- SWISS-MODEL - Protein Structure Homology-modelling Server
- Swiss-PdbViewer 4.1 - Analyze Several Proteins 3D Structure at the Same Time
- TASSER-Lite 1.0 - Protein Structure Modeling tool
- tCONCOORD 1.0 - Predict Protein Conformational Flexibility
- Tessellator 1.0 - Software for Tessellation of 3D Volume in Biological Molecule
- Theseus 3.3.0 - Superimpose Macromolecular Structures
- THREADER 3.51 - Protein Fold Recognition by Threading
- TimeScapes 1.5 - Molecular Dynamics Analysis tool
- Tinker 8.9.3 - Software Tools for Molecular Design
- Torsions - Calculates Backbone Torsion Angles from a PDB file
- TreePack 1.2 - Side Chain Assignment via Tree Decomposition
- TRITON 4.0 - Computational Aided Protein Engineering.
- Tuftsviewer / Molli 0.99 - Cross Platform Open Source PDB Viewer
- Twilight 1.13 - A tool for Ligand Density Validation
- UCSF Chimera 1.14 - Molecular Modeling System
- Uncoupler - Analysis of Coupled Folding and Binding
- UniCon3D 1.0 - United-residue Protein Folding via Stepwise, Probabilistic Sampling
- urms - Structure Comparison Algorithm
- USR-VS - Ligand-based Virtual Screening powered by Ultrafast Shape Recognition Techniques
- VASCo 1.0.2 - Computation and Visualization of Annotated Protein Surface Contacts
- VAST - Vector Alignment Search Tool
- VcPpt - Protein Ligend Docking & in silico High-throughput Screening
- VeaR - Geometry-based Structural Highlighter for Polypeptides
- VEGA ZZ 3.2.1.33 - Molecular Modeling Toolkit
- VESTA 3.5.7 - 3D Visualization System for Electronic & Structural Analysis
- Victor 1.0 - Virtual Construction Toolkit for Proteins
- Viewmol 2.4.1 - Molecule Viewer
- ViewMol3D 5.00.alpha.3 - 3D OpenGL Viewer for Molecular Structures
- VisGrid - Identify Pockets in Protein Surfaces
- VisualCNA 1.0 - Constraint Network Analysis and Protein Engineering
- Vivaldi - Visualisation, Analysis and Validation of NMR entries
- VMD 1.9.4 - Molecular Graphics Viewer
- Volarea 1.2 - VMD Plug-in to Measure the Surface and calculate the Volume of Proteins
- Voronoia 1.0 - Analyse Packing of Protein Structures
- Voroprot 0.7.6.7 - Explore Geomeric Features of Protein Structure
- VSDMIP pre-2.0 - Automated Structure & Ligand-based Virtual Screening Platform
- WAXSiS - Wide Angle X-ray Scattering in Solvent
- Webina 1.0.3 - A JavaScript/WebAssembly library that runs Vina in a browser
- webmol - Web Protein Viewer
- WHAT IF 8.3 - Protein Structure Analysis program
- WHISCY 1.02 - Predict Protein-protein Interfaces
- wLake 1.7 - Detecting Structural Water Molecules
- Wordom 0.22 rc3 - Analysis of Molecular Dynamics Simulations
- WPDB 2.2 - The Protein Data Bank Through Windows
- XCrySDen 1.6 - Crystalline & Molecular Structure Visualisation
- Xlink Analyzer v1.1.4 - Visualizing Cross-links on 3D Structures
- XLmap 0.2.1 - Visualize and Score Protein Structure Models based on sites of Protein Cross-linking
- XmMol 3.1 - Macromolecular Visualization and Modeling tool
- xPyder 201208 - Analyze Coupled Residues and their networks in Protein Structures
- XtalView 4.0 - Molecular Graphics Program
- YASARA 19.12.14 - Molecular Graphics, Modeling & Simulation program
- YUP 1.080827 / Yammp 2 - Molecular Simulation
- ZClass - Converts PDB file to a Voxelised Image
- ZDOCK 3.0.2 / M-ZDOCK - Protein Docking
- Zeus alpha - Java Multi-platform Molecular visualisation software
- ZMM 2020 - Molecular Modeling program for Theoretical studies of systems of any complexity
- Zodiac 0.6.5 - Molecular Modelling suite for Drug Design
- Category: Alignment / BLAST
- 3DCOMB 1.06 - Multiple Protein Structure Alignment
- aa2DNA - Align cDNA Sequences on the Basis of Protein Alignment
- ABMapper 2.0.4 - A suffix-array based Spliced Alignment tool
- abPOA v1.2.5 - adaptive banded Partial Order Alignment
- ABRA 0.97 - Assembly Based ReAligner
- ACANA - Accurate and Consistent Alignment Tool for DNA sequences
- ADEPT v1.0 - Domain Independent Sequence Alignment strategy for GPU architectures
- AFree 2.0 beta - Fast ALL versus ALL Proteome Comparisons
- AGE 0.4 - Optimal Alignment of Sequences with SVs
- AGILE 0.4.0 - AliGnIng Long rEads
- AgileQualityFilter 20121127 - Quality Control, Detagging and Reformatting of Clonal Sequencing data
- ALFALFA 0.8.1 - A Long Fragment Aligner
- Alfred v0.2.3 - BAM Alignment Statistics, Feature Counting and Annotation
- ALICAO - Contact-based Sequence Alignment
- ALICO 20100926 - Alignment Constrained Sampling
- ALIGN 2.0 - Pairwise Alignment
- Align 200807 - DNA Sequence Alignment Editor
- Align-m 2.3 - Multiple Sequence Alignment
- Alignancer 0.6 - Align Unaligned Regions in a HMMer-3 output alignments
- Alignathon - Multiple Whole Genome Alignment Testing Suite
- AlignBucket - Identify Optimized Subsets of Protein Sequences for Alignment
- AlignDist - Hacking the Alignment Distance
- AlignExIn 20130624 - Alignment Exon Intron Structure
- AlignMe 1.1 - Alignment of Membrane Proteins
- Alignment Benchmark - Collection of Protein Sequence Alignment Benchmarks
- AlignmentComparator 1.1.0 - Visualize and Annotate Differences between Alternative Multiple Sequence Alignments
- ALION 1.0 - Pairwise Sequence Alignment
- ALISS 1.2 - Alignment of Structures and Sequences
- AliView 1.27 - Alignment Viewer and Editor for large data sets
- ALN 3.5.2 - Pairwise Alignment of Biological Sequences Supporting Spliced Alignment Procedures
- aln3nn 0.6.0 - Multiple Alignment tool based on Alignment of Sequence Triplets
- AlnEdit 1.0 - Fast and Memory Efficient Alignment Editor
- ALNGG - Exon Finding by Genomic Sequence Comparison
- Alnpack 2.1 - C++ Library for Pairwise Local Alignment
- ALP 1.98 - Calculate Statistical Parameters in the modified Gumbel distribution for BLAST
- AlphaMALIG 1.1 - Aligns Sequences in a given Alphabet
- Alview 20160628 - Alignment View for BAM files
- ALVIS 0.1 - Explorative Analysis and Visualisation of Multiple Sequence Alignments
- AMPS D2.3a - Alignment of Multiple Protein Sequences
- AnABlast - Detect potential Coding Regions in DNA by Sequence Comparison
- Anchored DIALIGN 2.2.2 - Multiple Sequence Alignment with User-defined Constraints
- ANFO 0.98 - Mapper for Ancient DNA
- APoc 1.0 - Large-scale Structural Comparison of Protein Pockets
- AQUA 1.1 - Automatic Quality Improvment for Multiple Sequence Alignment
- ArchAlign 1.5 - Chromatin Alignment Algorithm for Detecting Chromatin Architecture
- ARIADNE 1.2 - Statistics of Sequence and Profile Alignments
- Arioc 1.43 - High-throughput Read Alignment with GPU-accelerated Exploration of Seed-and-extend Search Space
- ARRP 1.1 - Calculate Asymptotic and Robust Regression
- ASAP 0.1.2 - Align a Sequencing to two Genomes at the Same Time
- ASGAL v1.1.6 - Alternative Splicing Graph ALigner
- ASH 1.2 / RASH / GASH - Alignment of Structural Homologs
- ASpipe 2.1.8 - Process GeneSeqer/GMAP Alignments & Identify Alternative Splicing
- atlas-readpainter 0.9 - Multiple Alignment to Reference Tool
- AuberGene 1.1 - Sensitive Genome Alignment Tool
- BALSA - Bayesian Algorithm for Local Sequence Alignment
- BamView 1.2.11 - Display of Read Alignments in BAM Data Files
- BARCOD 1.0 - Multiple Alignment
- BarraCUDA 0.7.0 - Short Read Sequence Aligner using Graphics Processing Units
- Base-By-Base - Genome Pairwise & Multiple Alignment Editor
- BatAlign - A Short Read Aligner allowing Indels
- BatMis 3.00 - Basic Alignment Tool for Mismatches
- Bayes Aligner - Bayesian Adaptive Sequence Alignment Software
- BDBM 1.0.3 - BLAST DataBase Manager
- BEAP 0.6 beta - Blast Extension and Assembly Program
- BEDTools 2.30.0 - Compare Genomic Features
- BELLA v1.0 - Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper
- Belvu 20120403 - Multiple Alignments Viewer
- BFAST 0.7.0 - Alignment Tool for Large Scale Genome Resequencing
- BigBWA 1.0 - Approaching the Burrows-Wheeler Aligner to Big Data Technologies
- BigFoot - Bayesian Alignment and Phylogenetic Footprinting with MCMC
- BIMA v3 - Aligner customized for Mate Pair Library Sequencing
- Bio-samtools 2.6.2 - Ruby bindings for SAMtools
- BioParser 1.2.3 - Parsing Sequence Similarity Analysis Reports
- Bison 0.4.0 - Bisulfite Alignment On Nodes of a Cluster
- BitMapper 2.0.0.7 - Short Reads Alignment Tool
- BitPAl - Bit-parallel Alignment
- BL!P v2.0 - BLAST in Pivot
- Blasr - Basic Local Alignment with Successive Refinement
- BLAST 2.12.0 - Find Regions of Similarity between Sequences
- BlasterJS - JavaScript based BLAST Alignments Viewer
- BlasterQt 1.4 - Tool for BLAST and Sequence Extractions in Batch Mode
- blastgrep 1.0.2 - Grep for Pattern Matches but on Query-basis in BLAST reports
- BLASTO - BLAST on Orthologous groups
- BLASTPLOT 0.2 - Plot Blast Output Results
- BLAT 36 - Rapid mRNA/DNA & Cross-species Protein Alignments
- BlatView - Mapping EST's to Genomes
- Bowtie 1.3.0 / Bowtie2 2.4.4 - Ultrafast Memory-efficient Short Read Aligner
- BOXSHADE 3.2.3 - Pretty Printing and Shading of Multiple-Alignment files
- BRIG 0.95 - BLAST Ring Image Generator
- BS Seeker 2.1.8 - Mapping of Bisulfite-treated Short Reads
- BWA 0.7.17 - Burrows-Wheeler Aligner for Short and Long Reads.
- BWA-DoAll 1.0 - Batch Alignment and Processing of FASTQ libraries.
- BWBBLE - Short Read Alignment with Populations of Genomes
- BWT-SW 20080713 - Local Alignment tool for searching Nucleotide Sequences
- CAB-align - Residue-residue Contact Area Based Alignment
- CaBLASTP 1.0.3 - Performs BLAST on Compressed Proteomic data
- Cactus v2.0.1 - Genome Multiple Sequence Aligner
- CAPITAL 1.0.2 - Comparative Analysis of Pseudotime trajectory Inference with Tree ALignment
- CAST 1.2.2 - Compression-accelerated BLAST and BLAT
- CAT / Xat 0.8.6 - Cross-species Alignment Tool
- CBA 200504 - Consistency Based Alignment
- CBESW 20081023 - Sequence Alignment on the Playstation 3
- cblaster v1.3.11 - Find clustered hits from a BLAST search
- CCS - Biclustering analysis and detection of Condition-dependent Coexpression Network Modules
- CCT - CGView Comparison Tool
- CD-HIT 4.8.1 - Cluster Large Protein database at High Sequence Identity Threshold
- CEGA - Conserved Elements from Genomic Alignments
- Censor 4.2.29 - Compares and Masks Protein or Nucleotide Sequences
- Centrifuge 1.0.4-beta - Classifier for Metagenomic Sequences
- CGALN 1.2.3 - Pairwise Genomic Sequence Alignment Program
- CGAP-Align 0.1.1 - Time Efficient Read Alignment tool built on the top of BWA
- CHAIN 1.0.0 - Forging Evolutionary Links to Underlying Mechanisms
- ChromA 0.9 - Alignment for Chromatography Mass Spectrometry Data
- CHROMA 1.0 - Annotated Multiple Sequence Alignments
- CINEMA 5 0.2.1-BETA - Sequence Alignment Editor
- clasp 1.1 - Local Fragment Chainer using Sum-of-pair Gap Costs
- CLAST 0.1.5 - CUDA implemented large-scale Alignment search tool
- Clustal Omega 1.2.4 - Multiple Sequence Alignment
- ClustalW / ClustalX 2.1 - Multiple Sequence Alignment
- ClustalW-MPI 0.13 - ClustalW Analysis using Distributed and Parallel Computing
- CoCoNUT - Computational Comparative GeNomics Utilities Toolkit
- codaln 1.0 / code2aln 1.2 - Progressive Multiple Alignments of Partially Coding Sequences.
- CodonCode Aligner 9.0.2 - DNA Sequence Assembly & Alignment
- Cola a1 - Modular and Configurable Optimal Sequence Aligner
- COMA 1.10 - Detection of Distant Evolutionary Relationships
- Compare3D - Structure Alignment of Two or More Polypeptide Chains
- COMPASS 3.1 - COmparison of Multiple Protein Sequence Alignments with assessment of Statistical Significance.
- CONSAN 1.2 - Pairwise Structural RNA Alignment
- Consensus 20040414 - Web Interface for Finding DNA and Protein Patterns
- CONTRAlign 2.01 - CONditional TRAining for Protein Sequence Alignment
- ConvexAlign - Find Global Alignment between Multiple of networks
- CoreAligner - Multiple Genome Alignment for Core Genome Structure Identification
- CorreLogo 1.2.6 - 3D Sequence Logos of RNA and DNA Alignments
- Coval 1.5 - Improving the Quality of Short Read Alignment data
- CoverageTool 0.1 - Generate Artificial Sequence Constructs
- CPHmodels 3.2 - Protein Homology Modeling server
- CS-BLAST/ CSI-BLAST 2.2.3 - Sequence Context-specific Profiles for Homology Searching
- CSA - Cyclic DNA Sequence Aligner
- CTX-PSI-BLAST 1.0 / CTX-BLAST 1.0 - Context Sensitive version of Protein BLAST
- Cube - Comparative Analysis of Protein Sequences
- CUDA-BLASTP 2.0 - Accelerate BLASTP on CUDA-enabled Graphics Card
- CUDASW++ 3.1.2 - Parallel Smith Waterman Protein database search algorithm
- CUSHAW3 3.0.3 - Sensitive and Accurate Gapped Short-read Alignment
- cyclope 0.1 - Multiple circular DNA Sequence Alignments
- D2NGS - Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads
- D2Z 0.1 - Alignment Free Comparison of Regulatory Sequences
- dali_sp - Script for DaliLite to perform Serial Structure Comparison
- DAlign 0.9 - Computes the unit Cost Edit Distance between Haploids
- DANTE - Domain based ANnotation of Transposable Elements
- DART - Library includes a number of Bioinformatics Alignment Programs
- DCA 1.1 - Divide-and-Conquer Multiple Sequence Alignment
- deBGA - de Bruijn Graph-based Aligner
- DeepAlign 1.35 - Pairwise Protein Structure Alignment
- Delve 0.95 - A Probabilistic Short Read Aligner
- Destruct v0.4.19 - Accurate Rearrangement Detection using Breakpoint Specific Realignment
- DiagAF 21.2.7 - Pre-Alignment Filter for Sequence Alignment
- Dialign 2.2.1 / DIALIGN-TX 1.0.2 - Multiple Sequence Alignments
- DIAMOND v2.0.12 / AC-DIAMOND v1.0 - Accelerated BLAST compatible local Sequence Aligner
- Diamund - DIrect Alignment for MUtatioN Discovery
- DIDA 1.0.1 - Distributed and Parallel Indexing and Alignment algorithm
- DISSECT 1.0.2 - Transcriptome-to-Genome Alignment Tool
- DistanceSVM - Using Distances between Top-n-gram and Residue Pairs for Protein remote Homology Detection
- dmatch 0.1.8 - Alignment of single-cell RNA-seq samples using Density Matching
- Dotlet 1.5 - Comparing Sequences by Diagonal Plot Method
- DREAM-Yara - An exact Read Mapper for very large databases with short update time
- drFAST 1.0 - di-base Read Fast Alignment Search Tool
- Easyfig 2.2.5 - Genome Comparison Visualizer
- ERNE 2.1.1 - Extended Randomized Numerical alignEr
- ESPript 3.0.8 / ENDscript 2.0.10 - Generate Pretty PostScript Output from Aligned Sequences
- EST_GENOME 5.2 - Align a Spliced DNA Sequence to an Unspliced Genomic Sequence
- EulerAlign 0.9 - Alignment of DNA sequences using Eulerian graphs
- Exalign 1.0 - Gene Structural Alignments and Database Search
- Exonerate 2.2 - Generic Tool for Sequence Alignment
- FAAST 2.0.4 - Flowspace Assisted Alignment Search Tool
- Facet v1.4 - Multiple Alignment Accuracy Estimation and Parameter Advising
- FACS 2.1 - Align Sequences to a Reference Sequence
- FALP 1.06 - Calculation of the Gumbel Parameters for Frameshift Sequence Alignment
- FAST 20070903 - Fourier Transform based Algorithms for Significance Testing of ungapped Multiple Alignments
- FASTA 36.3.8h - Sequence Comparison
- FastSP 1.6.0 - Calculation of Alignment Accuracy
- FATCAT - Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists
- find_max_cover - Determine the best Combination of Local Alignments to a Query Sequence
- FOGSAA - Fast Optimal Global Sequence Alignment
- FOLDALIGN 2.5.2 / FOLDALIGNM 1.0.2 - RNA Structure and Sequence Alignment
- ForeSeqs 1.0.4 - Forecasting Missing Sequences for Multigene Alignments
- Formatt 1.0.1 - Correcting Protein Multiple Structural Alignments by Incorporating Sequence Alignment
- FR-HIT 0.7.1 - Recruit Metagenomic Reads to Homologous Reference Genome
- Fr-TM-align 201307 - Protein Structural Alignment
- FRESCO - Flexible Alignment with Rectangle Scoring Schemes
- Friend 2.0 - Multiple Structure Visualization & Multiple Sequence Alignment
- FRUUT 2.46 - Fast RNA Unrooted Unordered Tree Alignment
- FSA 1.15.9 - Fast Statistical Alignment
- FTALIGN - Fast Topology-independent and Global Structure Alignment through an FFT-based algorithm.
- Fuse - Multiple Network Alignment via Data Fusion
- G-BLASTN 1.1 - GPU-accelerated Nucleotide Alignment tool
- G-PAS 2.0 - Fast GPU vesion of a Pairwise Alignment algorithms
- Galinter 1.6 - Compare Protein-protein Interfaces
- Gambit 0.4.145 - Graphical BAM Alignment Viewer
- GapsMis 0.0.0 / GapMis 0.0.7 / GapMis-OMP 0.0.2 / libgapmis 0.0.9 - Pairwise Short-read Alignment
- GASSST 1.28 - Global Alignment Short Sequence Search Tool
- GAST - Global Alignment for Sequence Taxonomy
- GATA 0.7 - Graphic Alignment Tool for Comparative Sequence Analysis
- genBlastA 1.0.4 / genBlastG 1.39 - Homologous Gene Sequences
- GenePainter 2.0.5 - Mapping Gene Structures onto Protein Multiple Sequence Alignment
- GenomeMapper 0.4.4 - Short Read Mapping tool
- GenomeVISTA 2.0 - Integrated software package for Whole-genome Alignment and Visualization
- gff2aplot 2.0 - Visualizing Pair-wise Alignments with Annotated Axes from GFF files.
- GHOST-MP 1.3.4 - Parallel Sequence Similarity Search Tool
- GHOSTX 1.3.7 - Homology Search tool
- GHOSTZ 1.0.2 / GHOSTZ-GPU 1.1.0 - Homology Search tool
- Gibbs Motif Sampler 3.2 - Identify Motifs, Conserved Regions, in DNA or Protein Sequences
- GibbsCluster 2.0 - Simultaneous Alignment and Clustering of Peptide data
- GISMO 2.0 - Gibbs Sampler for Multi-alignment Optimization
- GLAM / AGLAM 2.1 - Gapless Local Alignment of Multiple Sequences
- GLASS - Aligns large Orthologous Genomic Regions
- Gmaj 20081103 - Interactive Viewer for Multiple Sequence Alignments
- GMAP / GSNAP 20210527 - Genomic Mapping and Alignment Program
- GNUMAP 3.0.2 - Genomic Next-generation Universal MAPper
- GPU-BLAST 1.1 - Sequence Alignment with GPUs
- GR-Align 1.5 - Aligning Protein Structures
- GRAPeFoot 20101217 - Pairwise (Genome) Re-aligner and Phylogenetic Footprinter
- GRASShopPER - de novo Assembly based on GPU Alignments
- GS-Aligner 1.0 - Large-scale Pairwise Sequence Alignment
- GUIDANCE 2.02 - Guide-tree based Alignment Confidence
- H-BloX 1.47N - Visualizing Alignment Block Entropies
- HAL 2.1 - Hierarchical Alignment Format API
- HAlign 2.1 - Fast Multiple Similar DNA/RNA Sequence Alignment
- HangOut - Generate Clean PSI-BLAST Profiles for Domains Containing long Insertions
- HAXAT 1.04 - Homopolymer Aware Cross Alignment Tool
- HHalign-Kbest 20150722 - Exploring Sub-optimal Alignments for remote Homology Comparative Modeling
- HHrepID 1.0.0 - de novo Protein Repeat Detection
- HISAT / HISAT2 2.1.0 - Hierarchical Indexing for Spliced Alignment of Transcripts
- HISEA - HIerarchical SEed Aligner
- Homed 6.8 - HOMologous sequence EDitor
- HOMOLENS r5 - Homologous Sequences in Ensembl Animal Genomes
- HoSeqI - Automated Homologous Sequence Identification in Gene Family Databases
- HPG Aligner 2.0.1 - NGS Read Mapping
- HS-BLASTN 0.0.5 - Accelerated MegaBLAST Search tool
- HtBackground - Building a Heterogeneous Background Model for DNA Multiple Alignments
- HubAlign - Alignment of Protein-protein Interaction Networks
- HybridPSI - enhanced PSI-BLAST based on Hybrid Alignment
- i-ADHoRe 3.0 - Detect Degenerated Genomic Homology
- iAlign 1.1 - Structural alignment for protein-protein
- iBWA 0.6.2 - Iterative Burrows-Wheeler Alignment
- iHMMune-align 20071126 - Hidden Markov model-based Alignment and Identification of Germline Genes
- InDelFixer 1.1 - An Insertion and Deletion Fixing Aligner for 454, Illumina and PacBio
- Indelign 2.0.4 - Probabilistically Annotating Indels in Multiple Alignments
- Infernal 1.1.4 - Inference of RNA Alignment
- InterEvol PyMOL Plugin 1.1 - Structure-oriented Exploration of Sequence Alignments
- InterEvScore / InterEvolAlign - Scoring Function for / Alignments and Query InterEvol database
- ISAS - Imagenix Sequence Alignment System
- JAGuaR 2.1 - Junction Alignment to Genome for Repositioning RNA-seq Reads
- JAligner 1.0 - Biological Local Pairwise Sequence Alignment
- Jalview 2.11.1.4 - Multiple Alignment Editor
- JDotter - Java Dot Plot Alignments
- JESAM 0.8.1 - Parallel Processing DNA Sequence Comparison and Clustering
- jpHMM 201503 - Compare a Sequence to a Multiple Alignment of a Sequence Family
- JProfileGrid 2.0.5 - Multiple Sequence Alignment tool that generates ProfileGrids
- JSAV 2.0 - JavaScript Sequence Alignment Viewer
- Kablammo - Web-based BLAST Results Visualizer
- Kalign 2.03 / Kalignvu 2.1 / Mumsa 1.0 - Multiple Sequence Alignment , Viewer & Quality Assessment
- KalignP 1.0 - Improved Multiple Sequence Alignments using Position specific Gap Penalties in Kalign2
- KMAD 1.15 - Knowledge Based Multiple Sequence Alignment for Intrinsically Disordered Proteins
- LAGAN 2.0 - Genomic Alignment
- Laj 070222 - Alignment Viewer
- LaJolla 2.2.1 - Peer Reviewed Algorithm for the 3D Alignment
- Lalnview 3.0 - Graphical Viewer for Pairwise Sequence Alignments
- lasseblaste - Sequence Blast
- LAST r992 - Genome-Scale Sequence Comparison
- LASTZ 1.04.03 - Program for Aligning DNA Sequences
- LGA 1.1 - Large Grain Alignment
- LGSFAligner 01 - Align two RNA Secondary Structures Locally
- LiBis 0.1.5 - An Ultrasensitive Alignment method for low input Bisulfite Sequencing
- LibrAlign 0.9.0 - Displaying and Editing Multiple Sequence Alignments and Attached Data
- LIGSIFT - Ligand Structural Alignment and Virtual Screening
- LocARNA 1.9.2.1 - Global and Local Alignment of RNA
- LOCK 2.0 - Vector-based Protein Structure Alignment
- LRD aligner - Rank-Based Sequence Aligners
- M-Coffee - Combination of Multiple Sequence Alignment Packages
- MACO 20060322 - Gapped-alignment Scoring tool for Comparing Transcription Factor Binding Sites
- MACSE 2.05 - Multiple Alignment of Coding SEquences
- MACSIMS 1.42 - Multiple Alignment of Complete Sequences Information Management System
- MAFFT 7.487 - Multiple Alignment Program
- Magma 1.0 - Multiple Aligner of Genomic Multiple Alignments
- MAGNA++ 20150130 - Maximizing Accuracy in Global Network Alignment
- Malakite - Automatic Detection of Aligned Blocks in a multiple Protein Alignment
- Maligner - Fast Ordered Restriction Map Aligner
- MALT 0.5.3 - MEGAN Alignment tool
- MaM 1.4.2 - Manipulate Multiple Alignments of Genomic Sequences
- MAMMOTH 1.2 / MAMMOTH-mult - Protein Structural Alignment
- Mandala 1.1.1 - Generate Seed Designs for Seeded Alignment Algorithms
- MAPGAPS 1.0.1 - Multiply-Aligned Profiles for Global Alignment of Protein Sequences
- MapMyFlu 2.0 - Blast-server for Influenza Sequences
- Maq 0.7.1 - Mapping and Assembly with Qualities
- Maqview 0.2.5 - Graphical Read Alignment Viewer
- MARS - Improving Multiple Circular Sequence Alignment Using Refined Sequences
- MASon rev12 - Million Alignments in Seconds
- MASon rev12 - Reduce the Computing Time of NGS Analysis Pipelines
- MassBlast v0.9.13 – Accelarate Genome and Transcriptome data analysis
- MASTR 1.0 - Multiple Alignment of STructural RNAs
- MatAlign V4A - Comparison, Alignment of PSSMs
- Matt 1.0 - Multiple Protein Structure Alignment program
- Mattbench 1.0 - Protein Structural Alignment Benchmark relies on the Matt
- Mauve 2.4.0 - Multiple Genome Alignments
- Maxflow 0.1.1 - Alignment of Protein Sequences based on Pairwise Consistency
- MaxSSmap v1 - GPU program for Mapping Divergent Short Reads to Genomes with the Maximum Scoring Subsequence
- MCScanX / MCScanX-transposed - Scan multiple Genomes to Identify Homologous Chromosomal Regions and more
- MDAT - Multiple Domain Alignment Tool
- MetaBinG 0.4 / MetaBinG2 - ultra-fast Metagenomic Sequence Classification system using GPUs
- MGA 20030318 - Multiple Genome Aligner
- MGAviewer 1.3.0 - MetaGenomic Alignment Viewer
- MICA-aligner r345 - Next-generation sequencing short reads aligner based on Intel MIC
- MicroRazerS 1.0 - Rapid Alignment of small RNA reads
- Minimap2 v2.23 - Pairwise Alignment for Nucleotide Sequences
- MISHIMA 2.3.1 - Method for Inferring Sequence History In Terms of Multiple Alignment
- MISTRAL - Multiple Protein Structural Alignment
- MitoScape v1.0 - Machine-learning workflow for Aligning mtDNA from NGS data
- MM-align 20130815 - Protein Complex Structural Alignment
- MO-SAStrE v2.0 - Multiobjective Optimization for Sequence Alignments based on Structural Evaluations
- modplus - script for Modeller to perform Sequence-structure Alignment
- ModuleAlign - Module-based Global Alignment of Protein-protein Interaction networks
- MORPH v0.1 beta - Probabilistic Alignment of Cis-regulatory Modules
- MOSAIK 2.2.3 - Aligner for Next-generation Sequencing Technologies
- MOSAL v.1 - Multiobjective Sequence Alignment
- MP-T 201407 - Membrane Protein Sequence-structure Alignment
- MPAlign-editor 3.0.0 - Graphical Tool for DNA and Protein Sequences and Alignments
- MPBLAST - Multiplex BLAST
- mpiCUDA-BLASTP 1.0 - Accelerate BLASTP for Scanning Protein Sequence databases on GPU clusters
- mrFAST 2.6.1.0 - Micro Read Fast Alignment Search Tool
- mrsFAST-Ultra 3.4.2 - Micro-read Substitution-only Fast Alignment Search Tool
- MS_Align 2.0 - Comparison of Minisatellites
- MS-BLAST - Mass Spectrometry driven BLAST
- msa 1.18.0 - An R Package for Multiple Sequence Alignment
- MSACompro 1.2.0 - Protein Multiple Sequence Alignment using predicted Secondary Structure
- MSAProbs 0.9.7 - Parallel and Accurate Multiple Sequence Alignment
- MSARC 1.2 - Multiple Sequence Alignment without Guide-trees
- MSAViewer 1.0.0 - Multiple Sequence Alignment Viewer
- MSAVis - Multiple Sequence Alignment Visualization system
- Mugsy 1.2.3 - Multiple Whole Genome Alignment tool
- Mulan - Multiple Sequence Alignment tool
- MultAlin 5.4.1 - Multiple Sequence Alignment
- Multi-Harmony - Multi-group Sequence Harmony & multi-Relief
- multiAlignFree 1.0 - Multiple Alignment-Free Sequence Comparison
- MultiGeneBlast 1.1.14 - Combined BLAST searches for Operons and Gene Clusters
- Multiz / TBA 20090121 - Multi-sequence Aligner Package
- MUMMALS 1.01 - MUltiple alignment with Multiple MAtch state models of Local Structure
- MUMmer 4.0.0Beta2 / pymummer 0.11.0 - Alignment of Large-scale DNA & Protein Sequences
- MUMmerGPU 2.0 - High-throughput sequence alignment using GPU
- Murlet 0.0.1 - Practical Alignment tool for structural RNA Sequences
- MUSCLE 3.8.31 - Multiple Sequence Alignment
- MUSTANG 3.2.3 - Multiple Structural Alignment Algorithm
- Mview 1.67 - Multiple Alignment Viewer
- mVISTA - Compare Sequences & Visualize Alignments with Annotation Information
- MXSCARNA 2.1 - Multiplex Stem Candidate Aligner for RNAs
- Myblast 1.0.29 - Customized Biological Sequence Alignment tool
- NanoOK 1.33 - Alignment and Analysis of Nanopore Reads
- NAP - Nucleotide Amino Acid Alignment
- NcDNAlign 1.0.7 - Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences
- Neighborhood Correlation 2.1 - Homology Identification
- NeoBio 1.0 pre-alpha - Sequence alignment algorithms in Java
- NETAL - Global Alignment of Protein-protein Interaction Networks
- NetCoffee - Alignment approach to Identify Functionally Conserved Proteins in Multiple Networks
- Nexalign 1.35 - Aligns Sequences to Databases
- Ngila 1.3 - Pairwise Alignments Using Evolutionary Models
- Nhunt 1.5.7 - Nucleic Acid Sequence Similarity search
- NOBLAST 2.1 / JAMBLAST 1.10 - extended NCBI BLAST programs / Manager
- noisy 1.5.12 - Identify Homo-plastic Characters in Multiple Sequence Alignments
- Novoalign 4.03.03 - Aligner Capable of Gapped Alignment for Illumina Short Reads
- NW 3.12 - Pairwise Needleman and Wunsch Sequence Alignment program
- NW-align - Protein Sequence-sequence Alignments
- OAT 0.91 - Similarity Measurement Tool for Genomes
- oculus 0.1.2 - Faster Sequence Alignment by Compression
- OD-seq 0.99.3 - Outlier Detection in Multiple Sequence Alignments
- OMA 0.98 - Optimal Multiple Sequence Alignment
- Opal v3.0 - Aligning multiple Biological Sequences
- Opscan - Comparing Genomes
- Ortheus 0.5 - Inference of Ancestor (aka tree) Alignments
- OrthoRBH 1.1 - Rapidly Identify Orthologous cDNA Sequences in related Species
- OSA 4.1.1.1 - Alignment tool for RNA-Seq
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