Align
- SMALT 0.7.4 – Align DNA Sequencing Reads with Genomic Reference Sequences
- Sim4 20121010 – Align an Expressed DNA Sequence with a Genomic Sequence
- LASTZ 1.03.34 – Program for Aligning DNA Sequences
- ShaEP 1.1.2.1036 – Align Two Rigid 3D Molecular Structure Models
- PepAligner 1.1.4034 – Align Protein Sequence
- ThreadPair 1.1 – Align Membrane Protein Sequences
- WAR – Webserver for Aligning structural RNAs
- PASS 2.02 – Align Short Sequences
- Alignancer 0.6 – Align Unaligned Regions in a HMMer-3 output alignments
- aa2DNA – Align cDNA Sequences on the Basis of Protein Alignment
- AGILE 0.4.0 – AliGnIng Long rEads
- SHRiMP 2.2.3 – Align Genomic Reads against Target genome
- BlastAlign 1.3 – Use Blast to Align Problematic Nucleotide Sequences
- ASAP 0.1.2 – Align a Sequencing to two Genomes at the Same Time
- Spa – Align cDNA sequences to Genome
- Nexalign 1.35 – Aligns Sequences to Databases
- M-align 2.8 – Align two time-series Microarray datasets using Time-warp or Gene-warp alignment matrices
- LGSFAligner 01 – Align two RNA Secondary Structures Locally
- ALIGN 1.1 – Pairwise Alignment
- AREM 1.0.1 – Aligning Short Reads from ChIP-sequencing by Expectation Maximization
- EST_GENOME 5.2 – Align a Spliced DNA Sequence to an Unspliced Genomic Sequence
- mmeta 1.0 – Align the TF-maps of Multiple Promoter Regions
- meta 1.1 – Align the TF-maps of two Gene Promoter Regions
- deepBlockAlign 1.0 – Align RNA-seq Profiles of Read Block Patterns.
- RSMatch 2.0 – Align RNA Secondary Structures and Motif Detection
- PHMMTS 20070918 – Aligns Sequence to Sequence of Known Secondary Structure
- doublet 1.0 – Incorporate Patterns of Dipeptide Covariation to Align Protein Sequences
- Sequoia 1.0.1 – Align Hpmologous Protein Sequences and Structures
- SUBOPT – Aligns Two Protein Sequences
- SIBsim4 0.20 – Align an Expressed DNA Sequence with a Genomic Sequence based Sim4
- Align 200807 – DNA Sequence Alignment Editor
- Gardenia – Compare & Align RNA Structures
- DnaSP 5.10.01 – Analysis of Nucleotide Polymorphism from Aligned DNA Sequence Data
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