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Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Updated: Apr 13, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Phylesystem: a git-based data store for community-curated phylogenetic estimates.

Emily Jane McTavish¹, Cody E Hinchliff², James F Allman³

¹Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA, Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany.

Bioinformatics (Oxford, England)

|May 6, 2015

Summary

This summary is machine-generated.

This study introduces open-source software for curating phylogenetic data, enhancing reproducibility and reuse. The system uses git for version control and GitHub for open access, facilitating community-driven data improvement.

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Last Updated: Apr 13, 2026

A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

Area of Science:

Evolutionary Biology
Bioinformatics

Background:

Archiving phylogenetic estimates is crucial for research transparency and reproducibility.
Existing platforms require data editing and taxonomic mapping for improved reusability.
Tracking curation provenance is essential for acknowledging contributions and correcting errors.

Purpose of the Study:

To develop software infrastructure for community-driven open curation of phylogenetic data.
To enhance the accuracy and reusability of published phylogenetic estimates.
To provide a transparent and version-controlled system for managing phylogenetic data.

Main Methods:

Developed a backend system using git for version control of phylogenetic data.
Utilized GitHub for hosting the data store, enabling open access.
Deployed a server running the 'phylesystem-api' to manage git and GitHub interactions.
Created a JavaScript web application for input and curation of phylogenetic statements.

Main Results:

Established a software infrastructure supporting open curation of phylogenetic data.
Implemented a system that preserves the history of edits through git's version control.
Provided open access to the data store via GitHub.
Deployed a functional web application for phylogenetic data curation.

Conclusions:

The developed system facilitates open and collaborative curation of phylogenetic data.
Enhanced data accuracy and reusability through version control and community input.
Promotes transparency and reproducibility in phylogenetic research.