title: GUIDANCE: a web server for assessing alignment confidence scores.
abstract: 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.
authors.affiliation: Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
authors.forename: Osnat
authors.initials: O
authors.lastname: Penn
authors.forename: Eyal
authors.initials: E
authors.lastname: Privman
authors.forename: Haim
authors.initials: H
authors.lastname: Ashkenazy
authors.forename: Giddy
authors.initials: G
authors.lastname: Landan
authors.forename: Dan
authors.initials: D
authors.lastname: Graur
authors.forename: Tal
authors.initials: T
authors.lastname: Pupko
mesh_terms: D054298:Human Immunodeficiency Virus Proteins / Q000737:chemistry; D020407:Internet; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry; D000086082:Viroporin Proteins
chemical_list: D054298:Human Immunodeficiency Virus Proteins; D054334:Viral Regulatory and Accessory Proteins; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins