An alignment confidence score capturing robustness to guide tree uncertainty.

By Osnat Penn, Eyal Privman, Giddy Landan, Dan-Ovidiu Graur, Tal Pupko. Molecular biology and evolution, 2010

346 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/4cf9979d9eff26ec9b87364d59e10f465a939f16

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In Molecular Biology

Citations in the corpus

A molecular phylogeny of Graphidaceae (Ascomycota, Lecanoromycetes, Ostropales) including 428 species (2013, methodology): “The unaligned MSA for the mtSSU and nuLSU gene partitions were also submitted to the GUIDANCE web server at http://guidance.tau.ac.il to assess alignment confidence scores for each site (Penn et al. 2010a, b).”
Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees (2016, background): “Alternative solutions are sometimes useful for assessing site-wise or overall reliability of an MSA, in systematic methods (e.g. Chang et al. , 2014; Penn et al. , 2010) or by manual inspection.”
Phylogeny of the Lobariaceae (lichenized Ascomycota: Peltigerales), with a reappraisal of the genus Lobariella (2013, methodology): “The alignments were submitted to the GUIDANCE server to delimit potential regions of alignment uncertainty (Penn et al. 2010a, b), and three ambiguously aligned regions of the mtSSU gene were removed and recoded with PICSORD (Lücking et al. 2011).”
A simple method to control over-alignment in the MAFFT multiple sequence alignment program (2016, methodology): “Possible applications include: (i) Increasing the diversity of MSAs to quantify residue-wise reliability in perturbation-based methods, such as HoT (Landan and Graur, 2007) or GUIDANCE (Penn et al. , 2010).”
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters (2015, methodology): “In this study, we aimed to systematically compare seven of the more recent algorithms to detect unreliable regions, GUIDANCE (26), HoT (21), ALISCORE (24), trimAl (22), TCS (31), ZORRO (29) and Noisy (20), on a wide range of both simulated and structure-based alignments.”
Ancient hybridizations among the ancestral genomes of bread wheat (2014, methodology): “A phylogenyaware sequence alignment pipeline modified from (19) was implemented in R language usingMAFFT (29) to construct multiple sequence alignments, GUIDANCE (30) to assess sequence alignment quality, and phangorn (31) to construct maximum likelihood topologies, which were used to evaluate ortho”