264 related articles for article (PubMed ID: 16789817)
1. Assessing the accuracy of ancestral protein reconstruction methods.
Williams PD; Pollock DD; Blackburne BP; Goldstein RA
PLoS Comput Biol; 2006 Jun; 2(6):e69. PubMed ID: 16789817
[TBL] [Abstract][Full Text] [Related]
2. A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families.
Pupko T; Pe'er I; Hasegawa M; Graur D; Friedman N
Bioinformatics; 2002 Aug; 18(8):1116-23. PubMed ID: 12176835
[TBL] [Abstract][Full Text] [Related]
3. Reconstruction of ancestral protein sequences and its applications.
Cai W; Pei J; Grishin NV
BMC Evol Biol; 2004 Sep; 4():33. PubMed ID: 15377393
[TBL] [Abstract][Full Text] [Related]
4. GeneTRACE-reconstruction of gene content of ancestral species.
Kunin V; Ouzounis CA
Bioinformatics; 2003 Jul; 19(11):1412-6. PubMed ID: 12874054
[TBL] [Abstract][Full Text] [Related]
5. Ancestral sequence alignment under optimal conditions.
Hudek AK; Brown DG
BMC Bioinformatics; 2005 Nov; 6():273. PubMed ID: 16293191
[TBL] [Abstract][Full Text] [Related]
6. Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference.
Krishnan NM; Seligmann H; Stewart CB; De Koning AP; Pollock DD
Mol Biol Evol; 2004 Oct; 21(10):1871-83. PubMed ID: 15229290
[TBL] [Abstract][Full Text] [Related]
7. Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates.
Ninio M; Privman E; Pupko T; Friedman N
Bioinformatics; 2007 Jan; 23(2):e136-41. PubMed ID: 17237082
[TBL] [Abstract][Full Text] [Related]
8. Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods.
Zhang J; Nei M
J Mol Evol; 1997; 44 Suppl 1():S139-46. PubMed ID: 9071022
[TBL] [Abstract][Full Text] [Related]
9. On the quality of tree-based protein classification.
Lazareva-Ulitsky B; Diemer K; Thomas PD
Bioinformatics; 2005 May; 21(9):1876-90. PubMed ID: 15647305
[TBL] [Abstract][Full Text] [Related]
10. Using ancestral sequences to uncover potential gene homologues.
Collins LJ; Poole AM; Penny D
Appl Bioinformatics; 2003; 2(3 Suppl):S85-95. PubMed ID: 15130821
[TBL] [Abstract][Full Text] [Related]
11. Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions.
Huang YM; Bystroff C
Bioinformatics; 2006 Feb; 22(4):413-22. PubMed ID: 16352653
[TBL] [Abstract][Full Text] [Related]
12. 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; 66(6):1054-1064. PubMed ID: 28057858
[TBL] [Abstract][Full Text] [Related]
13. A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor.
Brooks DJ; Fresco JR; Singh M
Bioinformatics; 2004 Sep; 20(14):2251-7. PubMed ID: 15073018
[TBL] [Abstract][Full Text] [Related]
14. Efficient parsimony-based methods for phylogenetic network reconstruction.
Jin G; Nakhleh L; Snir S; Tuller T
Bioinformatics; 2007 Jan; 23(2):e123-8. PubMed ID: 17237079
[TBL] [Abstract][Full Text] [Related]
15. Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation.
Sennett MA; Theobald DL
J Mol Evol; 2024 Apr; 92(2):181-206. PubMed ID: 38502220
[TBL] [Abstract][Full Text] [Related]
16. Align-m--a new algorithm for multiple alignment of highly divergent sequences.
Van Walle I; Lasters I; Wyns L
Bioinformatics; 2004 Jun; 20(9):1428-35. PubMed ID: 14962914
[TBL] [Abstract][Full Text] [Related]
17. Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions.
Gàlvez-Morante A; Guéguen L; Natsidis P; Telford MJ; Richter DJ
Genome Biol Evol; 2024 Apr; 16(4):. PubMed ID: 38518756
[TBL] [Abstract][Full Text] [Related]
18. Inferring property selection pressure from positional residue conservation.
Hoberman R; Klein-Seetharaman J; Rosenfeld R
Appl Bioinformatics; 2004; 3(2-3):167-79. PubMed ID: 15693742
[TBL] [Abstract][Full Text] [Related]
19. Bayesian search of functionally divergent protein subgroups and their function specific residues.
Marttinen P; Corander J; Törönen P; Holm L
Bioinformatics; 2006 Oct; 22(20):2466-74. PubMed ID: 16870932
[TBL] [Abstract][Full Text] [Related]
20. Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examples.
Tuller T; Birin H; Kupiec M; Ruppin E
J Comput Biol; 2010 Sep; 17(9):1327-44. PubMed ID: 20874411
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
