GUIDANCE: a web server for assessing alignment confidence scores

By Osnat Penn, Eyal Privman, Haim Ashkenazy, Giddy Landan, Dan-Ovidiu Graur, Tal Pupko. Nucleic Acids Res., 2010

641 citations recorded by the source corpus.

Evaluating the accuracy of multiple sequence alignment (MSA) is critical for virtually every comparative sequence analysis that uses an MSA as input. Here we present the GUIDANCE web-server, a user-friendly, open access tool for the identification of unreliable alignment regions. The web-server accepts as input a set of unaligned sequences. The server aligns the sequences and provides a simple graphic visualization of the confidence score of each column, residue and sequence of an alignment, using a color-coding scheme. The method is generic and the user is allowed to choose the alignment algorithm (ClustalW, MAFFT and PRANK are supported) as well as any type of molecular sequences (nucleotide, protein or codon sequences). The server implements two different algorithms for evaluating confidence scores: (i) the heads-or-tails (HoT) method, which measures alignment uncertainty due to co-optimal solutions; (ii) the GUIDANCE method, which measures the robustness of the alignment to guide-tree uncertainty. The server projects the confidence scores onto the MSA and points to columns and sequences that are unreliably aligned. These can be automatically removed in preparation for downstream analyses. GUIDANCE is freely available for use at http://guidance.tau.ac.il.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ffe61e2feda9410f967271aff0933ffdb48f2b26

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

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).”
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters (2015, methodology): “The GUIDANCE algorithm (25,26) generates alternative MSAs by utilizing the observation that alignments substantially vary when given alternative tree topologies to guide the progressive alignment.”
Building phylogenetic trees from molecular data with MEGA. (2013, background): “If you downloaded the sequences through your favorite web browser and saved them as a .fasta file that file can be used as the input for Guidance.”
Pitfalls in supermatrix phylogenomics (2017, positive): “This can even be extended, as done for instance in BMGE, GUIDANCE and FSA, to mask portions of sequences, which is particularly useful to detect annotation errors or frameshifts in coding sequences.”
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).”