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Items: 1 to 20 of 110

1.

Improving genome-wide scans of positive selection by using protein isoforms of similar length.

Villanueva-Cañas JL, Laurie S, Albà MM.

Genome Biol Evol. 2013;5(2):457-67. doi: 10.1093/gbe/evt017.

2.

Improving the specificity of high-throughput ortholog prediction.

Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS.

BMC Bioinformatics. 2006 May 28;7:270.

3.

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes.

Markova-Raina P, Petrov D.

Genome Res. 2011 Jun;21(6):863-74. doi: 10.1101/gr.115949.110. Epub 2011 Mar 10.

5.

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.

6.

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
7.

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.

Huber T, Faulkner G, Hugenholtz P.

Bioinformatics. 2004 Sep 22;20(14):2317-9. Epub 2004 Apr 8.

PMID:
15073015
8.
9.

POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.

Hongo JA, de Castro GM, Cintra LC, Zerlotini A, Lobo FP.

BMC Genomics. 2015 Aug 1;16:567. doi: 10.1186/s12864-015-1765-0.

10.

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
11.

PosiGene: automated and easy-to-use pipeline for genome-wide detection of positively selected genes.

Sahm A, Bens M, Platzer M, Szafranski K.

Nucleic Acids Res. 2017 Jun 20;45(11):e100. doi: 10.1093/nar/gkx179.

12.

On the quality of tree-based protein classification.

Lazareva-Ulitsky B, Diemer K, Thomas PD.

Bioinformatics. 2005 May 1;21(9):1876-90. Epub 2005 Jan 12.

PMID:
15647305
13.

Mulan: multiple-sequence local alignment and visualization for studying function and evolution.

Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W.

Genome Res. 2005 Jan;15(1):184-94. Epub 2004 Dec 8.

14.

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.

Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T.

Bioinformatics. 2009 Aug 1;25(15):1972-3. doi: 10.1093/bioinformatics/btp348. Epub 2009 Jun 8.

15.

Investigating selection on viruses: a statistical alignment approach.

de Groot S, Mailund T, Lunter G, Hein J.

BMC Bioinformatics. 2008 Jul 10;9:304. doi: 10.1186/1471-2105-9-304.

16.

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.

17.

Bayesian coestimation of phylogeny and sequence alignment.

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

BMC Bioinformatics. 2005 Apr 1;6:83.

18.

The effects of alignment error and alignment filtering on the sitewise detection of positive selection.

Jordan G, Goldman N.

Mol Biol Evol. 2012 Apr;29(4):1125-39. doi: 10.1093/molbev/msr272. Epub 2011 Nov 1.

PMID:
22049066
19.

HoSeqI: automated homologous sequence identification in gene family databases.

Arigon AM, Perrière G, Gouy M.

Bioinformatics. 2006 Jul 15;22(14):1786-7. Epub 2006 May 8.

PMID:
16682422
20.

IsoSel: Protein Isoform Selector for phylogenetic reconstructions.

Philippon H, Souvane A, Brochier-Armanet C, Perrière G.

PLoS One. 2017 Mar 21;12(3):e0174250. doi: 10.1371/journal.pone.0174250. eCollection 2017.

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