T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life
| Autor: | Georgiana May, Jana M. U'Ren, Jolanta Miadlikowska, François Lutzoni, A. Elizabeth Arnold, James B. White, Frank Kauff, Ignazio Carbone, Mark A. Miller |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Statistics and Probability Systematics Theoretical computer science Computer science Context (language use) Locus (genetics) Computational biology Biochemistry DNA sequencing 03 medical and health sciences Ascomycota Genus Phylogenetics Endophytes Subphylum Clade Molecular Biology Phylogeny Metadata Phylogenetic tree biology Amplicon biology.organism_classification Computer Science Applications Computational Mathematics Tree (data structure) 030104 developmental biology Taxon Computational Theory and Mathematics Genetic Loci Outgroup Sequence Alignment Software Function (biology) Pezizomycotina |
| Zdroj: | Bioinformatics. 33:1160-1168 |
| ISSN: | 1367-4811 1367-4803 |
| Popis: | Motivation High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades. Results In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi—Pezizomycotina (Ascomycota)—based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2). T-BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User-customizable metadata can be visualized on the tree. Availability and Implementation T-BAS Version 1.0 is available online at http://tbas.hpc.ncsu.edu. Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources. Supplementary information Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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