T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees-Reference-Cited by-同舟云学术

T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees

Published:2019-07-18 Issue:29 Volume:8 Page:
ISSN:2576-098X
Container-title:Microbiology Resource Announcements
language:en
Short-container-title:Microbiol Resour Announc

Author:

Carbone Ignazio¹,White James B.¹,Miadlikowska Jolanta²,Arnold A. Elizabeth³⁴,Miller Mark A.⁵,Magain Nicolas²⁶,U'Ren Jana M.⁷^ORCID,Lutzoni François²

Affiliation:

1. Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA

2. Department of Biology, Duke University, Durham, North Carolina, USA

3. School of Plant Sciences, The University of Arizona, Tucson, Arizona, USA

4. Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, Arizona, USA

5. San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, USA

6. Institut de Botanique B22, Biologie de l’Évolution et de la Conservation, UR InBios, Université de Liège, Liège, Belgium

7. Department of Biosystems Engineering, The University of Arizona, Tucson, Arizona, USA

Abstract

The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.

Funder

HHS | National Institutes of Health

National Science Foundation

Publisher

American Society for Microbiology

Subject

Genetics,Immunology and Microbiology (miscellaneous),Molecular Biology

Link

https://journals.asm.org/doi/pdf/10.1128/MRA.00328-19

Reference32 articles.

1. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life

2. A novel proof of concept for capturing the diversity of endophytic fungi preserved in herbarium specimens