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1
PSAR-align: improving multiple sequence alignment using probabilistic sampling.
Bioinformatics. 2014 Apr 1;30(7):1010-2. doi: 10.1093/bioinformatics/btt636. Epub 2013 Nov 12.
2
PSAR: measuring multiple sequence alignment reliability by probabilistic sampling.
Nucleic Acids Res. 2011 Aug;39(15):6359-68. doi: 10.1093/nar/gkr334. Epub 2011 May 16.
3
R3D Align: global pairwise alignment of RNA 3D structures using local superpositions.
Bioinformatics. 2010 Nov 1;26(21):2689-97. doi: 10.1093/bioinformatics/btq506. Epub 2010 Oct 6.
4
mTM-align: an algorithm for fast and accurate multiple protein structure alignment.
Bioinformatics. 2018 May 15;34(10):1719-1725. doi: 10.1093/bioinformatics/btx828.
5
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score.
BMC Bioinformatics. 2008 Dec 12;9:531. doi: 10.1186/1471-2105-9-531.
6
A performance enhanced PSI-BLAST based on hybrid alignment.
Bioinformatics. 2011 Jan 1;27(1):31-7. doi: 10.1093/bioinformatics/btq621. Epub 2010 Nov 24.
7
Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support.
Bioinformatics. 2006 Apr 1;22(7):885-6. doi: 10.1093/bioinformatics/btl028. Epub 2006 Feb 10.
8
CGAP-align: a high performance DNA short read alignment tool.
PLoS One. 2013 Apr 11;8(4):e61033. doi: 10.1371/journal.pone.0061033. Print 2013.
9
BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm.
Bioinformatics. 2014 Nov 15;30(22):3166-73. doi: 10.1093/bioinformatics/btu507. Epub 2014 Jul 29.
10
Comparative analysis of algorithms for next-generation sequencing read alignment.
Bioinformatics. 2011 Oct 15;27(20):2790-6. doi: 10.1093/bioinformatics/btr477. Epub 2011 Aug 19.

引用本文的文献

1
LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation.
BMC Bioinformatics. 2019 Dec 30;20(1):739. doi: 10.1186/s12859-019-3292-5.
2
Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments.
Mol Biol Evol. 2019 Oct 1;36(10):2340-2351. doi: 10.1093/molbev/msz142.
3
seq-seq-pan: building a computational pan-genome data structure on whole genome alignment.
BMC Genomics. 2018 Jan 15;19(1):47. doi: 10.1186/s12864-017-4401-3.
4
Portable and Error-Free DNA-Based Data Storage.
Sci Rep. 2017 Jul 10;7(1):5011. doi: 10.1038/s41598-017-05188-1.
5
Alignathon: a competitive assessment of whole-genome alignment methods.
Genome Res. 2014 Dec;24(12):2077-89. doi: 10.1101/gr.174920.114. Epub 2014 Oct 1.

本文引用的文献

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The UCSC Genome Browser database: extensions and updates 2013.
Nucleic Acids Res. 2013 Jan;41(Database issue):D64-9. doi: 10.1093/nar/gks1048. Epub 2012 Nov 15.
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PSAR: measuring multiple sequence alignment reliability by probabilistic sampling.
Nucleic Acids Res. 2011 Aug;39(15):6359-68. doi: 10.1093/nar/gkr334. Epub 2011 May 16.
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Upcoming challenges for multiple sequence alignment methods in the high-throughput era.
Bioinformatics. 2009 Oct 1;25(19):2455-65. doi: 10.1093/bioinformatics/btp452. Epub 2009 Jul 30.
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Fast statistical alignment.
PLoS Comput Biol. 2009 May;5(5):e1000392. doi: 10.1371/journal.pcbi.1000392. Epub 2009 May 29.
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Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.
Bioinformatics. 2009 Feb 1;25(3):295-301. doi: 10.1093/bioinformatics/btn630. Epub 2008 Dec 4.
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Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.
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Multiple sequence alignment using ClustalW and ClustalX.
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Recent evolutions of multiple sequence alignment algorithms.
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Measuring the accuracy of genome-size multiple alignments.
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Multiple sequence alignment: in pursuit of homologous DNA positions.
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