List of sequence alignment software

Known as: Burrows-Wheeler Aligner, Alignment program, Alignment 
This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence… (More)
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Highly Cited
2013
Highly Cited
2013
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or assembly contigs against a large reference genome… (More)
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Highly Cited
2010
Highly Cited
2010
Fast and accurate long-read alignment with Burrows–Wheeler transform
MOTIVATION Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most… (More)
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Highly Cited
2010
Highly Cited
2010
Parallelization of the MAFFT multiple sequence alignment program
SUMMARY Multiple sequence alignment (MSA) is an important step in comparative sequence analyses. Parallelization is a key… (More)
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Highly Cited
2009
Highly Cited
2009
SOAP2: an improved ultrafast tool for short read alignment
SUMMARY SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer… (More)
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Highly Cited
2009
Highly Cited
2009
Fast and accurate short read alignment with Burrows–Wheeler transform
MOTIVATION The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast… (More)
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Highly Cited
2007
Highly Cited
2007
High-throughput sequence alignment using Graphics Processing Units
The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the… (More)
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Highly Cited
2005
Highly Cited
2005
Kalign – an accurate and fast multiple sequence alignment algorithm
The alignment of multiple protein sequences is a fundamental step in the analysis of biological data. It has traditionally been… (More)
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Highly Cited
2002
Highly Cited
2002
Multiple sequence alignment using partial order graphs
MOTIVATION Progressive Multiple Sequence Alignment (MSA) methods depend on reducing an MSA to a linear profile for each alignment… (More)
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Highly Cited
1999
Highly Cited
1999
A comprehensive comparison of multiple sequence alignment programs
In recent years improvements to existing programs and the introduction of new iterative algorithms have changed the state-of-the… (More)
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Highly Cited
1999
Highly Cited
1999
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment
MOTIVATION The performance and time complexity of an improved version of the segment-to-segment approach to multiple sequence… (More)
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