Alignment / BLAST
- POA 2 – Multiple Sequence Alignment Using Partial Order Graphs
- SPLICE POA 20040610 – Splice Analysis using Partial Order Multiple Sequence Alignment
- Neighborhood Correlation 2.1 – Homology Identification
- SSW – SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications
- SCISSORS – Split-read Aligner
- MOSAIK 2.1.73 – Aligner for Next-generation Sequencing Technologies
- Gambit 0.4.145 – Graphical BAM Alignment Viewer
- MOSAL v.1 – Multiobjective Sequence Alignment
- CorreLogo 1.2.6 – 3D Sequence Logos of RNA and DNA Alignments
- Compareads 1.3 – Comparing Huge Metagenomic experiments
- BLAST / netBlast 2.2.28 – Find Regions of Similarity between Sequences
- Bowtie 2.10 – Ultrafast Memory-efficient Short Read Aligner
- MAFFT 7.037 – Multiple Alignment Program
- STRAP 20130226 – STRucture-based Sequence Alignment Program
- CUSHAW 2.4.2 – CUDA compatible Short Read Alignment
- PRANK 20130410 – Phylogeny-aware Progressive Sequence Alignment
- mrFAST 2.6.0.1 – Micro Read Fast Alignment Search Tool
- SeqTools 4.20 – A Suite of Tools for Visualising Sequence Alignments
- LAST r286 – Genome-Scale Sequence Comparison
- BamView 1.2.9 – Display of Read Alignments in BAM Data Files
- CUDASW++ 3.0.14 – Parallel Smith Waterman Protein database search algorithm
- GMAP / GSNAP 20130509 – Genomic Mapping and Alignment Program
- BioEdit 7.2.0 – Biological Sequence Alignment Editor
- Smolign – Spatial Motifs Based Multiple Protein Structure Alignment
- SlideSort v2 – All Pairs Similarity Search for Short Reads
- ABMapper 2.0.4 – A suffix-array based Spliced Alignment tool
- SMALT 0.7.4 – Align DNA Sequencing Reads with Genomic Reference Sequences
- Novoalign 3.00.03 – Aligner Capable of Gapped Alignment for Illumina Short Reads
- RAPSearch 2.10 – Fast Protein Similarity Search
- Sim4 20121010 – Align an Expressed DNA Sequence with a Genomic Sequence
- SequenceServer 0.8.5 – Set up a Local BLAST Web Server to Search & Share Sequence data
- LocARNA 1.7.6 – Global and Local Alignment of RNA
- CS-BLAST/ CSI-BLAST 2.0.16 – Sequence Context-specific Profiles for Homology Searching
- HHsearch 2.0.16 – Protein Homology Detection by HMM–HMM Comparison
- HHblits 2.0.16 – Homology Detection by Iterative HMM-HMM Comparison
- TM-align 20130508- Quick & Accurate Structural Alignment
- CodonCode Aligner 4.1.1 – DNA Sequence Assembly & Alignment
- Infernal 1.1rc2 – Inference of RNA Alignment
- BWA 0.7.4 – Burrows-Wheeler Aligner for Short and Long Reads.
- BWT-SW 20080713 – Local Alignment tool for searching Nucleotide Sequences
- SPALN 2.0.6 – Mapping and Alignment of a set of cDNA Sequences onto a Genomic Sequence
- RMBlast 20130227 – RepeatMasker compatible version of NCBI BLAST suite
- jCE/jFATCAT 2.9 – Calculate Structure Alignment
- Gibbs Motif Sampler 3.10 – Identify Motifs, Conserved Regions, in DNA or Protein Sequences
- LASTZ 1.03.34 – Program for Aligning DNA Sequences
- SAMtools 0.1.19 – Utilities for Manipulating Alignments in the SAM format
- ICM-Browser 3.7 2e – Molecules & sequence alignments Visualization
- Ribostral 20070223 – RNA Sequence Alignment Analysis program
- ARRP 1.0 – Calculate Asymptotic and Robust Regression
- ALP 1.8 – Calculate Statistical Parameters in the modified Gumbel distribution for BLAST
- SOrt-ITEMS – Sequence Orthology based approach for improved Taxonomic Estimation of Metagenomic Sequences
- SeaView 4.4.1 – Sequence Alignment and Phylogenetic Tree Building
- PepAligner 1.1.4034 – Align Protein Sequence
- ScalaBLAST 2.0.3 – Multiprocessor Implementation of the NCBI BLAST library
- AlignDist – Hacking the Alignment Distance
- StatAlign 2.1 – Bayesian Analysis of Protein, DNA and RNA Sequences
- SRmapper 0.1.5 – Genome-hashing Alignment tool
- ThreadPair 1.1 – Align Membrane Protein Sequences
- MP-T – Membrane Protein Sequence-structure Alignment
- YAP – Pairwise Sequence Alignment Using Secondary Structures
- APoc 1.0 – Large-scale Structural Comparison of Protein Pockets
- JProfileGrid 2.0.5 – Multiple Sequence Alignment tool that generates ProfileGrids
- Stellar 1.4 – Local Pairwise Aligner
- tantan 13 – Find Cryptic Repeats in DNA, RNA, and Protein Sequences.
- rna-star 2.3.0e – Spliced Transcripts Alignment to a Reference
- atlas-readpainter 0.9 – Multiple Alignment to Reference Tool
- PASH 3.0.6.2 – Large-scale Sequence Comparison Method
- CTX-PSI-BLAST 1.0 / CTX-BLAST 1.0 – Context Sensitive version of Protein BLAST
- Ngila 1.3 – Pairwise Sequences Alignment with Robust Evolutionary Models
- Maxflow 0.1.1 – Alignment of Protein Sequences based on Pairwise Consistency
- modplus – script for Modeller to perform Sequence-structure Alignment
- dali_sp – Script for DaliLite to perform Serial Structure Comparison
- Dali / DaliLite 3.3 – Structural Alignments between two Protein Structures
- PSI-BLAST-ISS 1.04 – The PSI-BLAST Intermediate Sequence Search tool
- Re-searcher 1.4 – System for Recurrent Searches of Homologs in Protein Sequence databases
- COMA 1.10 – Detection of Distant Evolutionary Relationships
- Vorometric – Integrated Search and Alignment of Protein Structures using Voronoi Contacts
- Mugsy 1.2.3 – Multiple Whole Genome Alignment tool
- W-curve – Visualization and Analysis of long Genomic Strings
- sStu 1.1 – Multiple kinds of Sequence Alignments
- PrimerMatch – PCR Primer Alignment Tools
- PeCoP – PSI-BLAST Sequence to find Persistently Conserved Positions
- SWeBLAST – Look for Recombinations in non-aligned Sequences using BLAST
- Supersplat 1.0 – Spliced RNA-seq Alignment
- ProAlign 0.5a3 – Probabilistic Multiple Alignment program
- DISSECT 1.0.2 – Transcriptome-to-Genome Alignment Tool
- TransposonPSI 20100822 – PSI-Blast to Mine (Retro-)Transposon ORF Homologies
- GUIDANCE 1.3.1 – Guide-tree based Alignment Confidence
- PSAweb – Analysis of Protein Sequence and Multiple Alignment
- GenomeMapper 0.4.4 – Short Read Mapping tool
- WHAM 0.1.5 – High-throughput Sequence Alignment
- BEDTools 2.17.0 – Compare Genomic Features
- SAP 1.1.3 – Pairwise Protein Structure Alignment via double Dynamic Programming
- MGAviewer 1.3.0 – MetaGenomic Alignment Viewer
- SNAP 20080926 – Non-sequential Pair-wise Structural Alignment
- MAPPIS 1.0 – Multiple 3D Alignment of Protein-Protein Interfaces
- MultiBind 1.0 – Multiple 3D Alignment of Binding Sites
- SiteEngine 1.0 – Pairwise 3D Alignment of Binding Sites
- STACCATO 1.2 – Structure Based Multiple Sequence Alignment
- mrsFAST 2.5.0.4 – Micro-read Substitution-only Fast Alignment Search Tool
- ReAlignerV 8.1.5 / REALIGNER 1.2 – Genomic Alignment Tool & Implementation
- PharmaGist 1.0 – Multiple flexible alignment of small drug-like ligand molecules
- I2I-SiteEngine 1.2 – Pairwise 3D Alignment of Protein-Protein Interfaces
- PALMapper 0.4 – Spliced Alignments of RNA-Seq Reads
- ERNE 1.2 – Extended Randomized Numerical alignEr
- rNA 1.0 / mrNA 1.0 / grNA 0.9 – randomized Numerical Aligner
- MaM 1.4.2 – Manipulate Multiple Alignments of Genomic Sequences
- HHomp – Homology Detection of OMPs by HMM-HMM Comparison
- Jalview 2.8 – Multiple Alignment Editor
- CAT / Xat 0.8.6 – Cross-species Alignment Tool
- Exalign 1.0 – Gene Structural Alignments and Database Search
- Splign 20100723 – Compute cDNA-to-Genomic / Spliced Sequence Alignment
- PASS 2.02 – Align Short Sequences
- SWPS3 20120914 – Smith-Waterman local Alignment Optimized Algorithm
- ProGraphMSA – Fast and Robust Phylogeny-Aware Multiple Sequence Alignment
- JESAM 0.8.1 – Parallel Processing DNA Sequence Comparison and Clustering
- StatSigMA beta / StatSigMA-w v2 – Computes P-value of (Whole-Genome) Multiple Alignment
- POSA – Partial Order Structure Alignment
- FATCAT – Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists
- SBG – Sorted Blast Graph
- alignexin – Alignment Exon Intron Structure
- NAIL – Network Analysis Interface for Linking HMMER results
- MS-BLAST – Mass Spectrometry driven BLAST
- SeSAW – Functional Mapping by Sequence-Derived Structural Alignment Weights
- ASH 1.2 – Alignment of Structural Homologs
- ParaAT 1.0 – Parallel Alignment & back-Translation
- Petunia SmRNA Blast – Tool for BLAST searching against Petunia Small RNAs
- blast2ps 0.3 – Graphical overview of Blast Output
- SQUARE – Server for Quick Alignment Reliability Evaluation
- SECISaln 1.0 – Create Structure-based Alignments of an extensive dataset of Eukaryotic SECIS Sequences
- CCT – CGView Comparison Tool
- SAS-Pro 201106 – Sequential and Non-sequential Structure Alignment of Proteins
- GPU-BLAST 1.1 – Sequence Alignment with GPUs
- MicroRazerS 1.0 – Rapid Alignment of small RNA reads
- Statmap 0.3.1 – Fast Alignment tool for Mapping Short Reads to a Reference Genome
- iHMMune-align 20071126 – Hidden Markov model-based Alignment and Identification of Germline Genes
- Alignancer 0.6 – Align Unaligned Regions in a HMMer-3 output alignments
- seg-suite 11 – Manipulate Segments and Alignments
- MSACompro 1.2.0 – Protein Multiple Sequence Alignment using predicted Secondary Structure
- RL-CSA 20101023 – Regular-language Constrained Pairwise Global Sequence Alignment
- FRUUT 2.40 – Fast RNA Unrooted Unordered Tree Alignment
- aa2DNA – Align cDNA Sequences on the Basis of Protein Alignment
- MUMMALS 1.01 – MUltiple alignment with Multiple MAtch state models of Local Structure
- PCMA – Profile Consistency Multiple sequence Alignment
- HangOut – Generate Clean PSI-BLAST Profiles for Domains Containing long Insertions
- COMPASS 3.1 – COmparison of Multiple Protein Sequence Alignments with assessment of Statistical Significance.
- PROMALS3D – Multiple Sequence and Structure Alignment Server
- SeqAlto 0.5-r123 – Fast and Accurate Read Alignment for Resequencing
- BLAT 35 – Rapid mRNA/DNA & Cross-species Protein Alignments
- QPALMA 0.9.3 – Optimal Spliced Alignments of Short Sequence Reads
- ISAS – Imagenix Sequence Alignment System
- X-MATE 1.0 – Mapping Short Read data
- BS Seeker 20100423 – Mapping of Bisulfite-treated Short Reads
- AGILE 0.4.0 – AliGnIng Long rEads
- mpiCUDA-BLASTP 1.0 – Accelerate BLASTP for Scanning Protein Sequence databases on GPU clusters
- CUDA-BLASTP 2.0 – Accelerate BLASTP on CUDA-enabled Graphics Card
- CBESW 20081023 – Sequence Alignment on the Playstation 3
- Parallel T-Coffee 1.914 – Parallel Multiple Sequence Aligner based on TCoffee
- Clustal Omega 1.1.0 – Multiple Sequence Alignment
- SHRiMP 2.2.3 – Align Genomic Reads against Target genome
- CGALN 1.2.2 – Pairwise Genomic Sequence Alignment Program
- BlastR 2.2 – Searching and Clustering RNA
- drFAST 1.0 – di-base Read Fast Alignment Search Tool
- Tmod 1.1.1 – Toolbox of Motif Discovery
- BlastViewer 2.4 – Blast Results Viewer
- JAligner 1.0 – Biological Local Pairwise Sequence Alignment
- BlastAlign 1.3 – Use Blast to Align Problematic Nucleotide Sequences
- jpHMM 201208 – Compare a Sequence to a Multiple Alignment of a Sequence Family
- ASpipe 2.1.8 – Process GeneSeqer/GMAP Alignments & Identify Alternative Splicing
- SAPS/SSPA 20110801 – Statistical Analysis of Protein Sequences & Significant Segment Pair Alignment
- MSAProbs 0.9.7 – Parallel and Accurate Multiple Sequence Alignment
- CD-HIT 4.6.1 – Cluster Large Protein database at High Sequence Identity Threshold
- GAST – Global Alignment for Sequence Taxonomy
- FR-HIT 0.7 – Recruit Metagenomic Reads to Homologous Reference Genome
- Samo 0.4.1 – Protein Structure Alignment tool based on Multiple Objective Optimization
- SANA – Protein Structure Alignment by Neighborhood Alignment
- SABIC – Protein Structure Alignment Based on Internal Coordinates
- ASAP 0.1.2 – Align a Sequencing to two Genomes at the Same Time
- PCPMer 3.5.6 – Determine Conserved Regions in multiple Sequence Alignments
- Myblast 1.0.29 – Customized Biological Sequence Alignment tool
- MASS 1.0 – Multiple Protein Structure Alignment by Secondary Structures
- MultiProt 1.0 – Multiple Protein Structure Alignment
- FlexProt – Pairwise Alignment of Flexible Protein Structures
- TriangleMatch – Pairwise Protein Structure Alignment based on Ca atoms
- GOSSIP – Global Structural Superposition of Proteins
- Spa – Align cDNA sequences to Genome
- MATLIGN 20060524 – Motif Clustering, Comparison and Matching tool
- Fr-TM-align 201106 – Protein Structural Alignment
- ViroBLAST – BLAST web interface
- TranslatorX – Nucleotide Sequence Alignment and Alignment Cleaning based on Amino Acid Information
- Nexalign 1.35 – Aligns Sequences to Databases
- SIB-BLAST – Algorithm to Improve Accuracy in PSI-BLAST Searches
- RevTrans 1.4 – Multiple Alignment of Coding DNA from Aligned Amino Acid Sequences
- PatMatch 1.2 – Find Patterns in Peptide and Nucleotide Sequences
- T-Coffee 9.03 – Multiple Sequence Alignment Tools
- PARALIGN 5.0 – Rapid and Sensitive Sequence Similarity Searches
- FAST 20070903 – Fourier Transform based Algorithms for Significance Testing of ungapped Multiple Alignments
- ALICO 20100926 – Alignment Constrained Sampling
- Censor 4.2.28 – Compares and Masks Protein or Nucleotide Sequences
- CoverageTool 0.1 – Generate Artificial Sequence Constructs
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