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Items: 1 to 20 of 88

1.

Measuring guide-tree dependency of inferred gaps in progressive aligners.

Capella-Gutiérrez S, Gabaldón T.

Bioinformatics. 2013 Apr 15;29(8):1011-7. doi: 10.1093/bioinformatics/btt095. Epub 2013 Feb 23.

2.

Phylogeny-aware alignment with PRANK.

Löytynoja A.

Methods Mol Biol. 2014;1079:155-70. doi: 10.1007/978-1-62703-646-7_10.

PMID:
24170401
3.
4.

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR.

Syst Biol. 2012 Jan;61(1):90-106. doi: 10.1093/sysbio/syr095. Epub 2011 Dec 1.

PMID:
22139466
5.

Characterization of pairwise and multiple sequence alignment errors.

Landan G, Graur D.

Gene. 2009 Jul 15;441(1-2):141-7. doi: 10.1016/j.gene.2008.05.016. Epub 2008 Jun 3.

PMID:
18614299
6.

Mind the gaps: evidence of bias in estimates of multiple sequence alignments.

Golubchik T, Wise MJ, Easteal S, Jermiin LS.

Mol Biol Evol. 2007 Nov;24(11):2433-42. Epub 2007 Aug 20.

PMID:
17709332
7.
8.

The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses.

Nelesen S, Liu K, Zhao D, Linder CR, Warnow T.

Pac Symp Biocomput. 2008:25-36.

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.

Joint Bayesian estimation of alignment and phylogeny.

Redelings BD, Suchard MA.

Syst Biol. 2005 Jun;54(3):401-18.

PMID:
16012107
11.

Phylogenetic assessment of alignments reveals neglected tree signal in gaps.

Dessimoz C, Gil M.

Genome Biol. 2010;11(4):R37. doi: 10.1186/gb-2010-11-4-r37. Epub 2010 Apr 6.

12.
13.

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.

14.

The tree alignment problem.

Varón A, Wheeler WC.

BMC Bioinformatics. 2012 Nov 9;13:293. doi: 10.1186/1471-2105-13-293.

15.

Using CLUSTAL for multiple sequence alignments.

Higgins DG, Thompson JD, Gibson TJ.

Methods Enzymol. 1996;266:383-402.

PMID:
8743695
16.
17.

Evolution and phylogenetic utility of alignment gaps within intron sequences of three nuclear genes in bumble bees (Bombus).

Kawakita A, Sota T, Ascher JS, Ito M, Tanaka H, Kato M.

Mol Biol Evol. 2003 Jan;20(1):87-92.

PMID:
12519910
18.

Comparing programs and methods to use for global multiple sequence alignment.

Mount DW.

Cold Spring Harb Protoc. 2009 Jul;2009(7):pdb.ip61. doi: 10.1101/pdb.ip61.

PMID:
20147201
19.

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.

20.

T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.

Carbone I, White JB, Miadlikowska J, Arnold AE, Miller MA, Kauff F, U'Ren JM, May G, Lutzoni F.

Bioinformatics. 2017 Apr 15;33(8):1160-1168. doi: 10.1093/bioinformatics/btw808.

PMID:
28003260

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