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Items: 1 to 20 of 101

1.

EvalMSA: A Program to Evaluate Multiple Sequence Alignments and Detect Outliers.

Chiner-Oms A, González-Candelas F.

Evol Bioinform Online. 2016 Nov 28;12:277-284. eCollection 2016.

2.

OD-seq: outlier detection in multiple sequence alignments.

Jehl P, Sievers F, Higgins DG.

BMC Bioinformatics. 2015 Aug 25;16:269. doi: 10.1186/s12859-015-0702-1.

3.

DivA: detection of non-homologous and very divergent regions in protein sequence alignments.

Zepeda Mendoza ML, Nygaard S, da Fonseca RR.

BMC Res Notes. 2014 Nov 18;7:806. doi: 10.1186/1756-0500-7-806.

4.

Protein multiple sequence alignment benchmarking through secondary structure prediction.

Le Q, Sievers F, Higgins DG.

Bioinformatics. 2017 May 1;33(9):1331-1337. doi: 10.1093/bioinformatics/btw840.

5.

msa: an R package for multiple sequence alignment.

Bodenhofer U, Bonatesta E, Horejš-Kainrath C, Hochreiter S.

Bioinformatics. 2015 Dec 15;31(24):3997-9. doi: 10.1093/bioinformatics/btv494. Epub 2015 Aug 26.

PMID:
26315911
6.

SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation.

Anderson CL, Strope CL, Moriyama EN.

BMC Bioinformatics. 2011 May 21;12:184. doi: 10.1186/1471-2105-12-184.

7.

Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing.

Walenz B, Florea L.

Bioinformatics. 2011 Jul 1;27(13):1869-70. doi: 10.1093/bioinformatics/btr285. Epub 2011 May 6.

8.

A non-independent energy-based multiple sequence alignment improves prediction of transcription factor binding sites.

Salama RA, Stekel DJ.

Bioinformatics. 2013 Nov 1;29(21):2699-704. doi: 10.1093/bioinformatics/btt463. Epub 2013 Aug 28.

PMID:
23990411
9.

Measuring the distance between multiple sequence alignments.

Blackburne BP, Whelan S.

Bioinformatics. 2012 Feb 15;28(4):495-502. doi: 10.1093/bioinformatics/btr701. Epub 2011 Dec 23.

PMID:
22199391
10.

ANDES: Statistical tools for the ANalyses of DEep Sequencing.

Li K, Venter E, Yooseph S, Stockwell TB, Eckerle LD, Denison MR, Spiro DJ, Methé BA.

BMC Res Notes. 2010 Jul 15;3:199. doi: 10.1186/1756-0500-3-199.

11.

Making automated multiple alignments of very large numbers of protein sequences.

Sievers F, Dineen D, Wilm A, Higgins DG.

Bioinformatics. 2013 Apr 15;29(8):989-95. doi: 10.1093/bioinformatics/btt093. Epub 2013 Feb 21.

PMID:
23428640
12.

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.

Löytynoja A, Goldman N.

BMC Bioinformatics. 2010 Nov 26;11:579. doi: 10.1186/1471-2105-11-579.

13.

BALCONY: an R package for MSA and functional compartments of protein variability analysis.

Płuciennik A, Stolarczyk M, Bzówka M, Raczyńska A, Magdziarz T, Góra A.

BMC Bioinformatics. 2018 Aug 14;19(1):300. doi: 10.1186/s12859-018-2294-z.

14.

Evaluation measures of multiple sequence alignments.

Gonnet GH, Korostensky C, Benner S.

J Comput Biol. 2000 Feb-Apr;7(1-2):261-76.

PMID:
10890401
15.

NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences.

Rose D, Hertel J, Reiche K, Stadler PF, Hackermüller J.

Genomics. 2008 Jul;92(1):65-74. doi: 10.1016/j.ygeno.2008.04.003. Epub 2008 Jun 3.

16.

Using CLUSTAL for multiple sequence alignments.

Higgins DG, Thompson JD, Gibson TJ.

Methods Enzymol. 1996;266:383-402.

PMID:
8743695
17.

PROMALS3D: a tool for multiple protein sequence and structure alignments.

Pei J, Kim BH, Grishin NV.

Nucleic Acids Res. 2008 Apr;36(7):2295-300. doi: 10.1093/nar/gkn072. Epub 2008 Feb 20.

18.

Quantifying the displacement of mismatches in multiple sequence alignment benchmarks.

Bawono P, van der Velde A, Abeln S, Heringa J.

PLoS One. 2015 May 19;10(5):e0127431. doi: 10.1371/journal.pone.0127431. eCollection 2015.

19.

MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments.

Collingridge PW, Kelly S.

BMC Bioinformatics. 2012 May 30;13:117. doi: 10.1186/1471-2105-13-117.

20.

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.

Schreiber F, Pick K, Erpenbeck D, Wörheide G, Morgenstern B.

BMC Bioinformatics. 2009 Jul 16;10:219. doi: 10.1186/1471-2105-10-219.

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