GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters
By Itamar Sela, Haim Ashkenazy, Kazutaka Katoh, Tal Pupko. Nucleic Acids Res., 2015
751 citations recorded by the source corpus.
Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http://guidance.tau.ac.il.
Subfields: Genetics, Molecular Biology, Paleontology
View Paper: https://www.semanticscholar.org/paper/276b2d8990a63a82606fc4eb723467adb4afb7fa
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In Genetics
In Molecular Biology
- Robert C. Edgar
- Asha J. Dissanayake
- J. Johansen
- J. Šmarda
- J. Komárek
- O. Strunecký
- Kazutaka Katoh
- Patrick D. Schloss
In Paleontology
Citations in the corpus
- Applied aspects of methods to infer phylogenetic relationships amongst fungi (2020, background): “The confidence score from GUIDANCE2 is a reflection of the robustness of the generated alignment.”
- Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny (2021, background): “More recent proposals along similar lines include 19,24,25 .”
- Phylogeny and taxonomy of Synechococcus-like cyanobacteria (2020, methodology): “The validity of the 260 selected protein alignments was tested using OD–seq (Jehl et al. 2015) and Guidance v. 2.02 (Sela et al. 2015) detecting no sequence outliers.”