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phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics.

Bioinformatics (Oxford, England)

|January 7, 2017

Summary

Selecting representative genomes for phylogenomic tree inference is streamlined with phyloSkeleton. This package automates genome selection, retrieval, and preparation for multiple sequence alignment, simplifying phylogenetic analysis.

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Area of Science:

Genomics
Bioinformatics
Evolutionary Biology

Background:

Inferring accurate phylogenomic trees requires careful selection of representative genomes.
The increasing volume of available genome sequences presents challenges in choosing appropriate taxa for phylogenetic analysis.
Manual genome selection is time-consuming and can be subjective.

Purpose of the Study:

To introduce phyloSkeleton, a computational package designed to simplify and automate the process of selecting representative genomes for phylogenomic studies.
To provide tools for efficient genome retrieval, annotation, marker identification, and preparation for multiple sequence alignment.

Main Methods:

The phyloSkeleton package utilizes rules based on taxonomy and genome assembly quality for organism selection.
It automates the retrieval of genomes from public databases like NCBI and JGI.
The package includes functionalities for genome annotation, identification of specific markers, and preparation of data for multiple sequence alignment.

Main Results:

phyloSkeleton offers a user-friendly approach to selecting a representative set of genomes for phylogenomic tree construction.
The package facilitates the integration of diverse genomic data by automating several pre-alignment steps.
It aims to reduce the tedium and potential bias associated with manual genome selection.

Conclusions:

phyloSkeleton provides an efficient solution for researchers needing to build phylogenomic trees from large datasets.
The package democratizes phylogenomic analysis by simplifying complex data preparation steps.
Automated genome selection and preparation are crucial for advancing large-scale phylogenetic studies.