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Pairwise nucleotide sequence alignment software tools | Comparative genomics

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…
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BLAT
Desktop
Web

BLAT BLAST-Like Alignment Tool

Finds genomic sequences that match a protein or DNA sequence submitted by the…

Finds genomic sequences that match a protein or DNA sequence submitted by the user. BLAT is a very fast sequence alignment tool similar to BLAST typically used for searching similar sequences within…

LASTZ
Desktop

LASTZ

Allows to attain efficiency adequate for aligning entire mammalian genomes and…

Allows to attain efficiency adequate for aligning entire mammalian genomes and to increase its sensitivity. LASTZ is designed to preprocess one sequence or set of sequences and to align several query…

SIBsim4
Desktop

SIBsim4

Aligns an expressed DNA sequence with a genomic sequence. SIBsim4 is an…

Aligns an expressed DNA sequence with a genomic sequence. SIBsim4 is an application based on sim4. The core program Sim4 was developed to perform such alignments under the assumption that the…

zPicture
Web

zPicture

Allows user to detect evolutionarily conserved regions (ECRs). zPicture is an…

Allows user to detect evolutionarily conserved regions (ECRs). zPicture is an automated alignment and visualization tool to generate reliable, highly sensitive single or multiple pairwise sequence…

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SPALN
Web
Desktop

SPALN

Allows users to map and align cDNA or protein sequences onto a whole genomic…

Allows users to map and align cDNA or protein sequences onto a whole genomic sequence (WGS). Spaln intends to improve automatic classification of alternative splicing and transcriptional initiation…

YASS
Desktop
Web

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.

Base-By-Base
Desktop

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.…

Wise2DBA
Web

Wise2DBA

Aligns two sequences under the assumption that the sequences share a number of…

Aligns two sequences under the assumption that the sequences share a number of colinear blocks of conservation separated by potentially large and varied lengths of DNA in the two sequences. Wise2DBA…

promoterwise
Web

promoterwise

Compares two DNA sequences allowing for inversions and translocations, ideal…

Compares two DNA sequences allowing for inversions and translocations, ideal for promoters. PromoterWise is an online method that is available for aligning sequences that are not co-linear.

Satsuma
Desktop

Satsuma

Satsuma is a sequence alignment program that finds sequence matches through…

Satsuma is a sequence alignment program that finds sequence matches through cross-correlation. The software can overcome two intrinsic problems inherent to seeded alignment approaches: (i) no…

Parasail
Desktop

Parasail Pairwise Sequence Alignment Library

Contains implementations of global, semi-global and local pairwise sequence…

Contains implementations of global, semi-global and local pairwise sequence alignment algorithms. Parasail uses a 375 query sequences with a speed of 136 billions cells update per second. It executes…

MUMmerGPU
Desktop

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.

Spaced Words
Desktop
Web

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 by…

SWIFT Suit
Desktop

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.

MCALIGN
Desktop

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.

AGA
Web
Desktop

AGA Advanced Genome Aligner

Helps is align an unknown nucleic acid sequence against a (reference) genome.…

Helps is align an unknown nucleic acid sequence against a (reference) genome. AGA is a method developed to align any nucleic acid sequence against any genome for which Coding Sequence feature…

MOSAL
Web
Desktop

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…

PipTools
Desktop

PipTools

Assists user in annotation of genes and putative regulatory elements in…

Assists user in annotation of genes and putative regulatory elements in pairwise alignments. PipTools allows identification of putative regulatory elements that stand out as having a high level of…

Ngila
Desktop

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.

GLASS
Web
Desktop

GLASS GLobal Alignment SyStem

Aligns pairs of homologous DNA sequences. GLASS is designed for aligning long,…

Aligns pairs of homologous DNA sequences. GLASS is designed for aligning long, divergent sequences that contain blocks of moderate to strong homology, such as orthologous/paralogous pairs of genes.…

ALN
Web
Desktop

ALN

Allows alignment of a pair of nucleotide, amino acid sequences or groups of…

Allows alignment of a pair of nucleotide, amino acid sequences or groups of sequences. ALN is a spliced alignment program that can use a generalized profile as template.

kmacs
Desktop
Web

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…

Cola
Desktop

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…

GapMis
Desktop

GapMis

A tool for pairwise sequence alignment with a single gap.

A tool for pairwise sequence alignment with a single gap.

GATA
Desktop

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…

neobio
Desktop

neobio

Provides a library gathering bioinformatics algorithms. Neobio mainly supplies…

Provides a library gathering bioinformatics algorithms. Neobio mainly supplies sequence alignment algorithms. The Application Programming Interface (API) is composed of three packages which allows…

zAlign
Desktop

zAlign

Obtains a global alignment between two sequences in quadratic time and space.…

Obtains a global alignment between two sequences in quadratic time and space. zAlign is a local sequence aligner, especially intended for use with large biological DNA sequences, with more than 1Mbp.…

seg-suite
Desktop

seg-suite

Contains a toolkit for arranging segments, alignments, and annotations of…

Contains a toolkit for arranging segments, alignments, and annotations of sequences. seg-suite performs composing alignments and is composed of a conversion program which transforms various formats…

JAligner
Web
Desktop

JAligner

Aligns biological pairwise sequences. JAligner uses affine gap penalty model to…

Aligns biological pairwise sequences. JAligner uses affine gap penalty model to proceed.

SIAS
Web

SIAS Sequence Identity And Similarity

Calculates pairwise sequence identity and similarity from multiple sequence…

Calculates pairwise sequence identity and similarity from multiple sequence alignments.

supermatcher
Desktop

supermatcher

Calculates approximate local pair-wise alignments of larger sequences.…

Calculates approximate local pair-wise alignments of larger sequences. supermatcher returns approximate alignments in a standard alignment file. A combination of a word-match and Smith-Waterman local…

wordmatch
Desktop

wordmatch

Finds regions of identity (exact matches) of two sequences. wordmatch reports…

Finds regions of identity (exact matches) of two sequences. wordmatch reports regions in a standard EMBOSS alignment file and in standard EMBOSS sequence feature files.

backtranseq
Desktop

backtranseq

Reads a protein sequence and writes the nucleic acid sequence it is most likely…

Reads a protein sequence and writes the nucleic acid sequence it is most likely to have come from. backtranseq back-translates a protein sequence to a nucleotide sequence. This emboss tool uses a…

stretcher
Desktop

stretcher

Calculates an optimal global alignment of two sequences using a modification of…

Calculates an optimal global alignment of two sequences using a modification of the classic dynamic programming algorithm which uses linear space. Stretcher is an Emboss tool that uses…

matcher
Desktop

matcher

Uses as Waterman-Eggert local alignment of two sequences. matcher identifies…

Uses as Waterman-Eggert local alignment of two sequences. matcher identifies local similarities in two input sequences using a rigorous algorithm based on Bill Pearson's align application. The…

needleall
Desktop

needleall

Reads a set of input sequences and compares them all to one or more sequences,…

Reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. needleall uses the Needleman-Wunsch alignment algorithm to…

LALIGN
Web

LALIGN

Compares two sequences looking for local sequence similarities. LALIGN produces…

Compares two sequences looking for local sequence similarities. LALIGN produces k best “non-intersecting” local alignments for any chosen k. It needs only O(M + N + K) space, where M and N are…

Needle
Web

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.

TIP
Desktop

TIP Traducción Inversa de Proteínas

Applies genetic algorithms to improve the backtranslation, by minimizing the…

Applies genetic algorithms to improve the backtranslation, by minimizing the difference of some coding statistics with respect to their average value in the target. TIP works on sequence files and…

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