Alignment / BLAST
- Tangram 0.2.2 – Structural Variation(SV) Detection based on MOSAIK Alignments
- CUSHAW 2.4.2 – CUDA compatible Short Read Alignment
- BamView 1.2.9 – Display of Read Alignments in BAM Data Files
- GMAP / GSNAP 20130509 – Genomic Mapping and Alignment Program
- BioEdit 7.2.0 – Biological Sequence Alignment Editor
- LocARNA 1.7.6 – Global and Local Alignment of RNA
- CodonCode Aligner 4.1.1 – DNA Sequence Assembly & Alignment
- SPALN 2.0.6 – Mapping and Alignment of a set of cDNA Sequences onto a Genomic Sequence
- SAMtools 0.1.19 – Utilities for Manipulating Alignments in the SAM format
- FLANK 1.0 – Calculate Statistical Parameters governing Over-extension of biologically related Alignments into surrounding random sequences.
- SATé 2.2.7 – Simultaneous Alignment and Tree Estimation
- phyutility 2.6 – Phyloinformatic Utility for Trees, Alignments, and Molecular data
- spinal – Scalable Protein Interaction Network Alignment
- SeaView 4.4.1 – Sequence Alignment and Phylogenetic Tree Building
- MPA 1.0 – Multiple Peak Alignment
- MP-T – Membrane Protein Sequence-structure Alignment
- rna-star 2.3.0e – Spliced Transcripts Alignment to a Reference
- GCAligner 1.0 – Alignment of Chemical data obtained by Gas Chromatography
- Maxflow 0.1.1 – Alignment of Protein Sequences based on Pairwise Consistency
- SimAssemblyStage1/2 0.2 – Assembly Alignment of Contigs
- Vorometric – Integrated Search and Alignment of Protein Structures using Voronoi Contacts
- Mugsy 1.2.3 – Multiple Whole Genome Alignment tool
- PrimerMatch – PCR Primer Alignment Tools
- Virusbanker 1.0 – MySQL database of Virus Sequences and Alignments
- Supersplat 1.0 – Spliced RNA-seq Alignment
- DISSECT 1.0.2 – Transcriptome-to-Genome Alignment Tool
- GUIDANCE 1.3.1 – Guide-tree based Alignment Confidence
- PharmaGist 1.0 – Multiple flexible alignment of small drug-like ligand molecules
- Splign 20100723 – Compute cDNA-to-Genomic / Spliced Sequence Alignment
- SWPS3 20120914 – Smith-Waterman local Alignment Optimized Algorithm
- alignexin – Alignment Exon Intron Structure
- ASH 1.2 – Alignment of Structural Homologs
- ParaAT 1.0 – Parallel Alignment & back-Translation
- SQUARE – Server for Quick Alignment Reliability Evaluation
- Al-Eigen – Contact Map Overlap by Alignment of Eigenvectors
- iHMMune-align 20071126 – Hidden Markov model-based Alignment and Identification of Germline Genes
- BAli-Phy 2.1.1 – Bayesian Alignment and Phylogeny estimation
- biomc2 1.9 – Detect recombination in DNA Sequence Alignments
- Alignancer 0.6 – Align Unaligned Regions in a HMMer-3 output alignments
- seg-suite 11 – Manipulate Segments and Alignments
- ForCon 1.0 – Conversion of Nucleic Acid & Amino Acid Sequence Alignments
- FASTA BLAST Scan 2.4 – FASTA & BLAST Alignment Conversion
- RADAR 1.1.5 – Rapid Automatic Detection and Alignment of Repeats in protein sequences
- BLAT 35 – Rapid mRNA/DNA & Cross-species Protein Alignments
- CYNTENATOR 20101005 – Progressive Gene Order Alignment of 17 Vertebrate Genomes
- Syntenator 2 – Multiple Gene Order Alignments with a Gene-specific Scoring Function
- JAligner 1.0 – Biological Local Pairwise Sequence Alignment
- ASpipe 2.1.8 – Process GeneSeqer/GMAP Alignments & Identify Alternative Splicing
- SAPS/SSPA 20110801 – Statistical Analysis of Protein Sequences & Significant Segment Pair Alignment
- MASS 1.0 – Multiple Protein Structure Alignment by Secondary Structures
- MultiProt 1.0 – Multiple Protein Structure Alignment
- TriangleMatch – Pairwise Protein Structure Alignment based on Ca atoms
- Fr-TM-align 201106 – Protein Structural Alignment
- TranslatorX – Nucleotide Sequence Alignment and Alignment Cleaning based on Amino Acid Information
- ALICO 20100926 – Alignment Constrained Sampling
- Time-warp 3.2 – Generate Alignment Matrices
- Gene-warp 3.2 – Generate Alignment Matrices, Explore Temporal Asynchrony in Expression of Orthologs
- ALTER 1.3.1 – ALignment File Format Converter
- PaPaRa 2.0 – PArsimony-based Phylogeny-Aware Read alignment program
- GapMis 0.0.7 / GapMis-OMP 0.0.2 / libgapmis 0.0.7 – Pairwise Short-read Alignment
- RUM 1.11 – Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper
- MSFACTs 1.0.1.3 – Metabolomics Spectral Formatting, Alignment and Conversion Tools
- ACANA – Accurate and Consistent Alignment Tool for DNA sequences
- LigAlign 1.0 – Ligand-based Active site Alignment and Analysis
- misfits 1.0 – Evaluate Goodness of Fit between Phylogenetic Model and Alignment
- Protein-DNA Interface Alignment – Interface Alignment between any Two Protein-DNA complexes
- LookSeq – Alignment Visualization, Browsing and Analysis of Genome Sequence data
- SSEA 1.1 – Secondary Structure Element Alignment
- EulerAlign 0.9 – Alignment of DNA sequences using Eulerian graphs
- LGA 1.1 – Large Grain Alignment
- LASWG 0.5 – Local Alignment Statistics with Gaps
- MetaPathwayHunter 1.1 – Alignment of Metabolic Pathways
- SSAHAsnp 1.01 – Sequence Search and Alignment by Hashing Algorithm
- ssahaEST 1.0.1 – Sequence Search and Alignment by Hashing Algorithm
- SSAHA2 2.5.5 – Sequence Search and Alignment by Hashing Algorithm
- sim4cc 20101122 – Cross-Species Spliced Alignment
- ViTO 20031125 – Protein Sequence Structure Alignments
- Spines 1.15 – C++ Software Package for Genomic Sequence Alignment and Analysis
- MapNext 1.0 – Alignment and SNP Detection of Short Sequence Reads
- SSAHA 2.5.5 – Sequence Search & Alignment by Hashing Algorithm
- MapView 3.4.1 – Visualization of Short Reads Alignment
- BFAST 0.7.0 – Alignment Tool for Large Scale Genome Resequencing
- MUMmer 3.23 – Alignment of Large-scale DNA & Protein Sequences
- H-BloX 1.47N – Visualizing Alignment Block Entropies
- XMatchView 0.2 – Visualize DNA Sequence Alignments.
- PASsiT 1.0 – Post Alignment SNV Tools
- RSpredict – Predict Secondary Structures of multiple RNA Sequence Alignments
- Pairagon 1.1 – Pair-HMM based cDNA-to-genome Alignment
- ARTS – Alignment of RNA Tertiary Structures
- aln3nn 0.6.0 – Multiple Alignment tool based on Alignment of Sequence Triplets
- ConStruct 3.2.5 – RNA Alignment Editor and Consensus Structure Prediction Tool
- Murlet 0.0.1 – Practical Alignment tool for Structural RNA Sequences
- ALISS 1.2 – Alignment of Structures and Sequences
- NW-align – Protein Sequence-sequence Alignments
- PLAST 1.0 – Parallel Local Alignment Search Tool for Database Comparison
- GASSST 1.28 – Global Alignment Short Sequence Search Tool
- NAST-iEr 20110519 – Sequence Alignment Tool
- BALSA – Bayesian Algorithm for Local Sequence Alignment
- ALION 1.0 – Pairwise Sequence Alignment
- CBA 200504 – Consistency Based Alignment
- zPicture / multi-zPicture – Dynamic Alignment & Visualization Tool
- PipMaker/MultiPipMaker 20110812 – Alignments of Similar Regions in Sequences
- TOADS – TOpologies in Alignments of DNA Sequences
- Sigma 2.0 BETA – Non-coding DNA Sequence Alignment
- SeqVis 1.5 – Visualization of Compositional Heterogeneity in Large Alignments of Nucleotides
- CHROMA 1.0 – Annotated Multiple Sequence Alignments
- SnS-Align – Alignment of Distantly related Proteins
- Topali 2.5 – Statistical & Evolutionary Analysis of Multiple Sequence Alignments
- Align-m 2.3 – Multiple Sequence Alignment
- Laj 070222 – Alignment Viewer
- Mauve 2.3.1 – Multiple Genome Alignments
- Lalnview 3.0 – Graphical Viewer for Pairwise Sequence Alignments
- GeneDoc 2.7.0 – Multiple Sequence Alignment Editor
- Align 200807 – DNA Sequence Alignment Editor
- Squint 1.02 – Multiple Sequence Alignment Editor
- SHiAT 1.1 – Generates Plots of Variation along Sequence Alignment
- Se-Al 2.0a11 – Manual Sequence Alignment Editor
- VarPlot 1.2 – Similarity Plotting for Alignment of Sequences
- Quasar 1.2 – Score & Rank Sequence-structure Alignments
- PAT 0.9 – Protein Alignment Tool
- MetaPAT 20070215 – Tool for the Alignment of Metabolic Pathways
- SCALI – Non-sequential Structure-based Alignment
- ProSplign 20070709 – Alignment of Proteins against Genomic Sequences
- SRMA 0.1.15 – Sequence Re-alignment for Next Generation Sequencing
- PALS 1.0 – Pairwise Alignment of Long Sequences
- QuickAlign 1.03 – Alignment editor for Macinthosh computers
- TSDA 1.0 – Alignment tool to Analyse Recombinant DNA Sequences
- SWIFT 1.0.1 / BALSAM 1.3 – Fast Local Alignment Searching
- ChromA 0.9 – Alignment for Chromatography Mass Spectrometry Data
- AMPS D2.3a – Alignment of Multiple Protein Sequences
- NAP – Nucleotide Amino Acid Alignment
- JDotter – Java Dot Plot Alignments
- Palign – Alignment / Threading Program
- MUMmerGPU 2.0 – High-throughput sequence alignment using GPU
- MatAlign V4A – Comparison, Alignment of PSSMs
- D2Z 0.1 – Alignment Free Comparison of Regulatory Sequences
- EMMA 1.1 – Prediction & Alignment of Cis-regulatory Modules
- mVISTA – Compare Sequences & Visualize Alignments with Annotation Information
- GLAM / AGLAM 2.1 – Gapless Local Alignment of Multiple Sequences
- PutGaps Beta – DNA Gapped File from Amino Acid Alignment
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