Pairwise sequence alignment has received a new motivation due to the advent of recent patents in next-generation sequencing technologies, particularly so for the application of re-sequencing---the assembly of a genome directed by a reference sequence. Source text: Flouri et al.,…
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Desktop app
MultiObjective… MultiObjective Sequence Alignment Tools

MOSAL MultiObjective Sequence Alignment Tools

A pruning technique for improving the performance of dynamic programming…

A pruning technique for improving the performance of dynamic programming algorithms for bicriteria pairwise sequence alignment, which uses lower and upper bounds to discard states in early stages of…

Desktop app
Graphic Alignment… Graphic Alignment Tool for comparative sequence…

GATA Graphic Alignment Tool for comparative sequence Analysis

A standalone, platform independent, graphic alignment tool for comparative…

A standalone, platform independent, graphic alignment tool for comparative sequence analysis. GATA uses the NCBI-BLASTN program and extensive post-processing to identify all small sub-alignments…

Desktop app
Contiguous optimal… Contiguous optimal local aligner

Cola Contiguous optimal local aligner

Implements different optimal alignment algorithms, also allowing for scoring…

Implements different optimal alignment algorithms, also allowing for scoring contiguous matches of nucleotides in a nonlinear manner. The latter places more emphasis on short, highly conserved…

Desktop app
Web app
kmacs kmacs

kmacs

A computational method to alignment-free sequence comparison. kmacs calculates…

A computational method to alignment-free sequence comparison. kmacs calculates one generalized enhanced suffix array for each pair of sequences, so its run time is quadratic in the number of…

Desktop app
Web app
Spaced Words Spaced Words

Spaced Words

A package to alignment-free sequence comparison. Spaced Words uses one or a…

A package to alignment-free sequence comparison. Spaced Words uses one or a whole set pattern of care and doesn't care positions : the occurrence of a spaced word in a sequence is then defined…

Desktop app
Base-By-Base Base-By-Base

Base-By-Base

A whole genome pairwise and multiple alignment editor. The program highlights…

A whole genome pairwise and multiple alignment editor. The program highlights differences between pairs of alignments and allows the user to easily navigate large alignments of similar sequences.…

Desktop app
MCALIGN MCALIGN

MCALIGN

An improved pair-hidden-Markov-Model (pair HMM) based method for performing…

An improved pair-hidden-Markov-Model (pair HMM) based method for performing global pairwise alignment of non-coding DNA sequences.

Desktop app
Satsuma Satsuma

Satsuma

A highly parallelized program for high-sensitivity, genome-wide synteny.

A highly parallelized program for high-sensitivity, genome-wide synteny.

Desktop app
SWIFT Suit SWIFT Suit

SWIFT Suit

A program for fast local alignment search, guaranteeing to find epsilon-matches…

A program for fast local alignment search, guaranteeing to find epsilon-matches between two sequences.

Desktop app
Web app
YASS YASS

YASS

A DNA local alignment tool based on an efficient and sensitive filtering…

A DNA local alignment tool based on an efficient and sensitive filtering algorithm.

Desktop app
GapMis GapMis

GapMis

A tool for pairwise sequence alignment with a single gap.

A tool for pairwise sequence alignment with a single gap.

Web app
Needle Needle

Needle

Reads two input sequences and writes their optimal global sequence alignment to…

Reads two input sequences and writes their optimal global sequence alignment to file.

Desktop app
MUMmerGPU MUMmerGPU

MUMmerGPU

An open-source high-throughput parallel pairwise local sequence alignment…

An open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs) in common workstations.

Desktop app
Ngila Ngila

Ngila

A global alignment program that can align pairs of sequences using logarithmic…

A global alignment program that can align pairs of sequences using logarithmic and affine gap penalties.

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