Sequence
- RJESuite 20130412 – Sequence Analysis Utilities
- project – Projects Genomic Features onto their Sequences
- CLC Genomics Workbench 6.0.3 – Assembly & Analysis of Sequencing Data
- Matcher – Analyze whether Sequence contains Repeated Pattern
- BLAST / netBlast 2.2.28 – Find Regions of Similarity between Sequences
- SKAT 0.83 – SNP-set (Sequence) Kernel Association Test
- BioEdit 7.2.0 – Biological Sequence Alignment Editor
- CS-BLAST/ CSI-BLAST 2.0.16 – Sequence Context-specific Profiles for Homology Searching
- DNA Baser 3.5.4 – DNA Sequence Assembly & Analysis
- FASTA Unique Sequences 1.0 – Uniques the Sequences in a FASTA file
- FASTA Length 1.0 – Finds the Lengths of Sequences in a FASTA file
- FASTA Composition 1.0 – Find Overall Composition of Sequence
- SeqMaT – Sequence Manipulation Tool for Phylogenetic Analysis
- SeaView 4.4.1 – Sequence Alignment and Phylogenetic Tree Building
- Quality Filter – Filter Sequences based on Phred Quality
- ThreadPair 1.1 – Align Membrane Protein Sequences
- MP-T – Membrane Protein Sequence-structure Alignment
- Strelka 0.4.10.2 – Somatic Small-variant Calling from Sequenced Tumor-normal Sample Pairs
- SubSeqer – Detection and Identification of Repetitive Elements in low-complexity Sequences
- Chromas Lite 2.1 / Chromas 2.4 / ChromasPro 1.74 – Sequence & Chromatogram Editor
- MEME 4.9.0 – Discovering Motifs within the Sequences
- CLEVER 1.0 – Sequence based Approximation of Protein Energies
- modplus – script for Modeller to perform Sequence-structure Alignment
- bam2fastq 1.1.0 – Extract Sequences from a BAM file in Fastq format
- Paraclu 9 – Find Clusters in Data attached to Sequences
- SubMito 1.1 – Predict Protein Submitochondria Locations from Sequence
- Triplet-SVM – Predict a query sequence with Hairpin Structure as a real miRNA precursor or not
- TableParser – Extract Sequences from Tab-delimited Assembly Alignment Files
- Circoletto 20121015 – Visualize Sequence Similarity with Circos
- STAP – Sequence To Affinity Prediction
- PeCoP – PSI-BLAST Sequence to find Persistently Conserved Positions
- Jannotatix 0.8 – Sequence and Annotation Viewer
- OrientationChecker 1.0 – Check Orientation of 16S rRNA Gene Sequences
- SQPR 8.01 – Sequence Quality Plate Reader
- MetAl 1.1 – Calculate Metric Distances between Alternative Alignments of the same Sequences
- Weeder 1.4.2 – Motif Discovery in Sequences from Coregulated Genes of a Single Species
- HATSEQ / HAT – Hypergeometric Analysis of Tiling-arrays and SEQuence data
- CLOSET r78 – CLoud Open SequencE clusTering
- GP 0.26 / Arka 0.11 – Sequence Manipulation tools
- IceLogo 1.2 – Next-generation Visualization of Protein Consensus Sequences
- SRS3D 1.4 – System for Displaying 3D Structures integrated with Sequences and Features
- Ampred – Predict the Antimicrobial Activity of given Sequence
- Seq-Gen 1.3.3 – Simulate the Evolution of Sequences along a Phylogeny
- GeneStudio™ Pro 2.2.0.0 – Sequence Format Conversion Engine and More
- SeqVerter 2.0.4.4 – Sequence File Format Conversion Utility
- ForCon 1.0 – Conversion of Nucleic Acid & Amino Acid Sequence Alignments
- SESAME 1.0 – Analyze Amplicon Sequences obtained through NGS Technologies
- ANCESCON – ANCEStral sequence reCONstruction
- FaBox 1.40 – Online FASTA Sequences Toolbox
- jpHMM 201208 – Compare a Sequence to a Multiple Alignment of a Sequence Family
- GS De Novo Assembler – de novo DNA Sequence Assembly
- IRiS – Identification of Recombinations in Sequences
- PROCSE 2.0 – Probabilistic Clustering of Sequences
- POBO 20050518 – Screen predetermined Cis-elements from a set of sequences
- Nexalign 1.35 – Aligns Sequences to Databases
- Swelfe – Detector of Internal Repeats in Sequences and Structures
- TAXNAMECONVERT 2.4 – Rename Sequence and Taxon names in Tree and Sequence files
- SVA 1.10 – Sequence Variant Analyzer
- SCONE 0.61 – Sequence CONservation Evaluation
- WH – Fit Speciation Model to DNA Sequence data sets
- GRASP 2 -Visualization of Macromolecular Structures and Sequences
- AgdbNet 1.0.4 – Antigen Sequence database software for Web-based Bacterial Typing
- MochiView 1.45 – Genomic Sequences Browser
- MUpro 1.1 – Prediction of Protein Stability Changes for Single Site Mutations from Sequences
- RNAcontext – Predict the Sequence and Structure Preferences of RNA-binding proteins
- ARIADNE 1.2 – Statistics of Sequence and Profile Alignments
- cBar 1.2 – Identification of Chromosomal Sequence Fragments from Metagenome data
- R’MES 3.1.0 – Finding Exceptional Motifs in Sequences
- MiRfold 0.2b – Search for a good miRNA-like Folding in Sequence
- CAP3 / PCAP – Sequence and Genome Assembly Programs
- THOR 1.0 – Assemble Target Genomic Sequence Orthologs
- Sdiscover – Tool for Finding Motifs in Sequences
- SOKOS/CAN 20070522 – Sequence Oriented Kernels over SCFG with Genome Scanning Capability
- ALISS 1.2 – Alignment of Structures and Sequences
- NAST-iEr 20110519 – Sequence Alignment Tool
- CompareProspector – Sequence Motif Finding Algorithm
- PipMaker/MultiPipMaker 20110812 – Alignments of Similar Regions in Sequences
- BioSeqAnalyzer 1.0 – Analyze DNA and Protein Sequences
- SMS 2 – Sequence Manipulation Suite
- GeneDoc 2.7.0 – Multiple Sequence Alignment Editor
- PersonalGenBank 200610 – Local Sequence Database
- Align 200807 – DNA Sequence Alignment Editor
- Metasim 0.9.5 – Sequencing Simulator for Genomes and Metagenomes
- 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
- SimPlot 3.5.1 – Sequence Similarity Plotting
- MargFreq 1.02 – Calculate Marginal Frequencies at each Position of a Nucleotide/Amino Acid Sequence
- Vised 1.1 – Sequence Editor / Display Software
- goldMINER 2.0.27 – Use CDD to Automate Sequence Annotation
- ProSplign 20070709 – Alignment of Proteins against Genomic Sequences
- Bio2MIDI 2.1 – Convert DNA or Protein Sequence to MIDI file
- SRMA 0.1.15 – Sequence Re-alignment for Next Generation Sequencing
- PALS 1.0 – Pairwise Alignment of Long Sequences
- Evolver – Whole-genome Sequence Evolution Simulator
- SomaticCall 1.13 – Find Substitutions between Sequence Data
- SSU-ALIGN 0.1 – Structural Alignment of SSU rRNA Sequences
- SimiTri 1.0 – Visualise Similarity Relationships for Groups of Sequences
- CLOBB 2.0 – Cluster Sequences on the Basis of BLAST
- DIYA 1.0.1 – Microbial Genome Sequences Annotation
- AutoEditor 1.20 – Automated Correction of Genome Sequence Errors
- MUMmerGPU 2.0 – High-throughput sequence alignment using GPU
- paircomp 1.0 – Ungapped Comparisons of Two Sequences
- FamilyRelations II 20070330 – Comparative Sequence Analysis
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