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Related Experiment Video

Updated: Jan 27, 2026

Substructure Analyzer: A User-Friendly Workflow for Rapid Exploration and Accurate Analysis of Cellular Bodies in Fluorescence Microscopy Images

Substructure Analyzer: A User-Friendly Workflow for Rapid Exploration and Accurate Analysis of Cellular Bodies in Fluorescence Microscopy Images

Published on: July 15, 2020

GToTree: a user-friendly workflow for phylogenomics.

Michael D Lee¹

¹Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA.

Bioinformatics (Oxford, England)

|March 14, 2019

Summary

This summary is machine-generated.

GToTree is a new command-line tool simplifying phylogenomic tree construction for biologists. It integrates diverse genomic data and provides tree outputs, enhancing accessibility for researchers without extensive bioinformatics expertise.

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Published on: July 8, 2014

Area of Science:

Genomics
Evolutionary Biology
Bioinformatics

Background:

Phylogenomics is crucial for biological research, but computational hurdles limit its accessibility.
Existing tools require significant bioinformatics expertise for data integration and analysis.

Purpose of the Study:

Introduce GToTree, a user-friendly command-line tool for phylogenomic tree construction.
Democratize phylogenomic analysis for researchers with limited bioinformatics backgrounds.

Main Methods:

GToTree accepts various input formats (FASTA, GenBank, NCBI accessions).
It automates data processing, including filtering and alignment.
Includes 13 new single-copy gene (SCG) set Hidden Markov Models (HMMs) for bacterial and archaeal genomes.

Main Results:

GToTree generates alignment files, genome completeness, and redundancy estimates.
Produces phylogenomic trees based on user-specified SCG sets.
Successfully processed ~12,000 bacterial and archaeal genomes.

Conclusions:

GToTree significantly lowers the barrier to entry for conducting phylogenomic analyses.
Empowers a broader range of biologists to infer evolutionary relationships from genomic data.