4.7 Article

Cydrasil 3, a curated 16S rRNA gene reference package and web app for cyanobacterial phylogenetic placement

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

Ivica Letunic et al.

Summary: The Interactive Tree Of Life is an online tool for displaying, manipulating, and annotating phylogenetic and other trees. The latest version 5 introduces a new tree display engine and several new features, such as a new dataset type and expanded annotation options. Users can now also manually annotate trees by hand, providing more flexibility and control.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities

I-Min A. Chen et al.

Summary: The Integrated Microbial Genomes & Microbiomes system at the DOE's Joint Genome Institute contains annotated genome datasets and metagenome bins, with advanced search functions and a new statistical analysis tool available in IMG v 6.0. The updated web user interface includes a Help page and webinar tutorials to assist users in understanding and utilizing various IMG functions and tools in their research. New datasets have been processed with an extended prokaryotic annotation pipeline v.5, featuring expanded protein family assignments.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

Diego Darriba et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Microbiology

International Code of Nomenclature of Prokaryotes Prokaryotic Code (2008 Revision)

Charles T. Parker et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2019)

Article Evolutionary Biology

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Pierre Barbera et al.

SYSTEMATIC BIOLOGY (2019)

Article Multidisciplinary Sciences

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

Paula B. Matheus Carnevali et al.

NATURE COMMUNICATIONS (2019)

Article Biochemical Research Methods

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

Alexey M. Kozlov et al.

BIOINFORMATICS (2019)

Letter Biotechnology & Applied Microbiology

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen et al.

NATURE BIOTECHNOLOGY (2019)

Article Multidisciplinary Sciences

Taxonomy annotation and guide tree errors in 16S rRNA databases

Robert Edgar

Article Multidisciplinary Sciences

On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria

Rochelle M. Soo et al.

SCIENCE (2017)

Article Multidisciplinary Sciences

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Karthik Anantharaman et al.

NATURE COMMUNICATIONS (2016)

Article Evolutionary Biology

An Expanded Genomic Representation of the Phylum Cyanobacteria

Rochelle M. Soo et al.

GENOME BIOLOGY AND EVOLUTION (2014)

Article Biochemical Research Methods

Infernal 1.1: 100-fold faster RNA homology searches

Eric P. Nawrocki et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Christian Quast et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

Patrick M. Shih et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemical Research Methods

Aligning short reads to reference alignments and trees

Simon A. Berger et al.

BIOINFORMATICS (2011)

Article Evolutionary Biology

The origin of multicellularity in cyanobacteria

Bettina E. Schirrmeister et al.

BMC EVOLUTIONARY BIOLOGY (2011)

Article Biochemical Research Methods

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

Frederick A. Matsen et al.

BMC BIOINFORMATICS (2010)

Article Biochemical Research Methods

How Many Bootstrap Replicates Are Necessary?

Nicholas D. Pattengale et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Patrick D. Schloss et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)