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Items: 1 to 20 of 144

1.

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.

Löytynoja A, Goldman N.

Science. 2008 Jun 20;320(5883):1632-5. doi: 10.1126/science.1158395.

3.

Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment.

Kim J, Sinha S.

Bioinformatics. 2007 Feb 1;23(3):289-97. Epub 2006 Nov 15.

PMID:
17110370
4.

The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection.

Fletcher W, Yang Z.

Mol Biol Evol. 2010 Oct;27(10):2257-67. doi: 10.1093/molbev/msq115. Epub 2010 May 5.

PMID:
20447933
5.

HIV/SIV glycoproteins: structure-function relationships.

Douglas NW, Munro GH, Daniels RS.

J Mol Biol. 1997 Oct 17;273(1):122-49.

PMID:
9367752
6.

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees.

Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T.

Science. 2009 Jun 19;324(5934):1561-4. doi: 10.1126/science.1171243.

7.

Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin.

Zhang M, Gaschen B, Blay W, Foley B, Haigwood N, Kuiken C, Korber B.

Glycobiology. 2004 Dec;14(12):1229-46. Epub 2004 Jun 2.

PMID:
15175256
9.

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
10.

A model of evolution and structure for multiple sequence alignment.

Löytynoja A, Goldman N.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3913-9. doi: 10.1098/rstb.2008.0170.

11.

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction.

Westesson O, Barquist L, Holmes I.

Bioinformatics. 2012 Apr 15;28(8):1170-1. doi: 10.1093/bioinformatics/bts058. Epub 2012 Jan 28.

12.

indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels.

Strope CL, Scott SD, Moriyama EN.

Mol Biol Evol. 2007 Mar;24(3):640-9. Epub 2006 Dec 8.

PMID:
17158778
14.

Simultaneous statistical multiple alignment and phylogeny reconstruction.

Fleissner R, Metzler D, von Haeseler A.

Syst Biol. 2005 Aug;54(4):548-61.

PMID:
16085574
16.
17.

Joint Bayesian estimation of alignment and phylogeny.

Redelings BD, Suchard MA.

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

PMID:
16012107
18.

Evolution of relative synonymous codon usage in Human Immunodeficiency Virus type-1.

Meintjes PL, Rodrigo AG.

J Bioinform Comput Biol. 2005 Feb;3(1):157-68.

PMID:
15751118
19.

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
20.

Cirripede phylogeny using a novel approach: molecular morphometrics.

Billoud B, Guerrucci MA, Masselot M, Deutsch JS.

Mol Biol Evol. 2000 Oct;17(10):1435-45.

PMID:
11018151

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