These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
5. Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map. Ezawa K BMC Bioinformatics; 2016 Mar; 17():133. PubMed ID: 26992851 [TBL] [Abstract][Full Text] [Related]
6. Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences. Di Franco A; Poujol R; Baurain D; Philippe H BMC Evol Biol; 2019 Jan; 19(1):21. PubMed ID: 30634908 [TBL] [Abstract][Full Text] [Related]
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. PubMed ID: 18296485 [TBL] [Abstract][Full Text] [Related]
9. Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments. Ali RH; Bogusz M; Whelan S Mol Biol Evol; 2019 Oct; 36(10):2340-2351. PubMed ID: 31209473 [TBL] [Abstract][Full Text] [Related]
10. Characterization of pairwise and multiple sequence alignment errors. Landan G; Graur D Gene; 2009 Jul; 441(1-2):141-7. PubMed ID: 18614299 [TBL] [Abstract][Full Text] [Related]
11. SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation. Anderson CL; Strope CL; Moriyama EN BMC Bioinformatics; 2011 May; 12():184. PubMed ID: 21600033 [TBL] [Abstract][Full Text] [Related]
12. 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. PubMed ID: 24694831 [TBL] [Abstract][Full Text] [Related]
13. MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments. Collingridge PW; Kelly S BMC Bioinformatics; 2012 May; 13():117. PubMed ID: 22646090 [TBL] [Abstract][Full Text] [Related]
14. An alignment confidence score capturing robustness to guide tree uncertainty. Penn O; Privman E; Landan G; Graur D; Pupko T Mol Biol Evol; 2010 Aug; 27(8):1759-67. PubMed ID: 20207713 [TBL] [Abstract][Full Text] [Related]
17. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Sela I; Ashkenazy H; Katoh K; Pupko T Nucleic Acids Res; 2015 Jul; 43(W1):W7-14. PubMed ID: 25883146 [TBL] [Abstract][Full Text] [Related]
18. Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty. Chatzou M; Floden EW; Di Tommaso P; Gascuel O; Notredame C Syst Biol; 2018 Nov; 67(6):997-1009. PubMed ID: 30295908 [TBL] [Abstract][Full Text] [Related]
19. Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction. Ashkenazy H; Sela I; Levy Karin E; Landan G; Pupko T Syst Biol; 2019 Jan; 68(1):117-130. PubMed ID: 29771363 [TBL] [Abstract][Full Text] [Related]