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Items: 1 to 20 of 100

1.

Alignment Modulates Ancestral Sequence Reconstruction Accuracy.

Vialle RA, Tamuri AU, Goldman N.

Mol Biol Evol. 2018 Jul 1;35(7):1783-1797. doi: 10.1093/molbev/msy055.

2.

Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map.

Ezawa K.

BMC Bioinformatics. 2016 Mar 18;17:133. doi: 10.1186/s12859-016-0945-5.

3.

Class of multiple sequence alignment algorithm affects genomic analysis.

Blackburne BP, Whelan S.

Mol Biol Evol. 2013 Mar;30(3):642-53. doi: 10.1093/molbev/mss256. Epub 2012 Nov 9.

PMID:
23144040
4.

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
5.

Robustness of ancestral sequence reconstruction to phylogenetic uncertainty.

Hanson-Smith V, Kolaczkowski B, Thornton JW.

Mol Biol Evol. 2010 Sep;27(9):1988-99. doi: 10.1093/molbev/msq081. Epub 2010 Apr 5.

6.

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
7.

Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction.

Yang K, Zhang L.

Nucleic Acids Res. 2008 Mar;36(5):e33. doi: 10.1093/nar/gkn075. Epub 2008 Feb 22.

8.

Multiple sequence alignment averaging improves phylogeny reconstruction.

Ashkenazy H, Sela I, Levy Karin E, Landan G, Pupko T.

Syst Biol. 2018 May 15. doi: 10.1093/sysbio/syy036. [Epub ahead of print]

PMID:
29771363
9.
10.

ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability.

Arenas M, Weber CC, Liberles DA, Bastolla U.

Syst Biol. 2017 Nov 1;66(6):1054-1064. doi: 10.1093/sysbio/syw121.

PMID:
28057858
11.

Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees.

Groussin M, Hobbs JK, Szöllősi GJ, Gribaldo S, Arcus VL, Gouy M.

Mol Biol Evol. 2015 Jan;32(1):13-22. doi: 10.1093/molbev/msu305. Epub 2014 Nov 4.

12.

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
13.

Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty.

Md Mukarram Hossain AS, Blackburne BP, Shah A, Whelan S.

Genome Biol Evol. 2015 Jul 1;7(8):2102-16. doi: 10.1093/gbe/evv127.

14.

Multiple Sequence Alignment Based on a Suffix Tree and Center-Star Strategy: A Linear Method for Multiple Nucleotide Sequence Alignment on Spark Parallel Framework.

Su W, Liao X, Lu Y, Zou Q, Peng S.

J Comput Biol. 2017 Dec;24(12):1230-1242. doi: 10.1089/cmb.2017.0040. Epub 2017 Nov 8.

PMID:
29116822
15.

Reconstruction of ancestral protein sequences and its applications.

Cai W, Pei J, Grishin NV.

BMC Evol Biol. 2004 Sep 17;4:33.

16.

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
17.

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.

18.

A Novel Approach to Multiple Sequence Alignment Using Multiobjective Evolutionary Algorithm Based on Decomposition.

Zhu H, He Z, Jia Y.

IEEE J Biomed Health Inform. 2016 Mar;20(2):717-27. doi: 10.1109/JBHI.2015.2403397. Epub 2015 Feb 12.

PMID:
25700475
19.

TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction.

Chang JM, Di Tommaso P, Notredame C.

Mol Biol Evol. 2014 Jun;31(6):1625-37. doi: 10.1093/molbev/msu117. Epub 2014 Apr 1.

PMID:
24694831
20.

Ancestral Sequence Reconstruction as a Tool for the Elucidation of a Stepwise Evolutionary Adaptation.

Straub K, Merkl R.

Methods Mol Biol. 2019;1851:171-182. doi: 10.1007/978-1-4939-8736-8_9.

PMID:
30298397

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