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Updated: Jan 25, 2026

Microfluidic Tools for Probing Fungal-Microbial Interactions at the Cellular Level

Microfluidic Tools for Probing Fungal-Microbial Interactions at the Cellular Level

Published on: June 23, 2022

Fungal Phylogenomics.

Robert Riley¹, Laszlo Nagy²

¹United States Department of Energy Joint Genome Institute, Walnut Creek, CA, USA. rwriley@lbl.gov.

Methods in Molecular Biology (Clifton, N.J.)

|June 8, 2018

Summary

This summary is machine-generated.

Phylogenomics uses genomic data to reconstruct evolutionary histories. This study details methods for identifying gene families and analyzing them to build accurate species trees.

Keywords:

Fungi Genomics MCL clustering Orthologs Phylogenetic tree Phylogenomics Phylogeny inference Protein families

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Area of Science:

Genomics and evolutionary biology.
Computational biology and bioinformatics.

Background:

Phylogenomics reconstructs organismal evolutionary relationships using genomic data.
Understanding gene and protein evolution offers insights into biological functions.

Purpose of the Study:

To present minimal protocols for gene family inference.
To utilize gene families in phylogenomic analyses for species tree reconstruction.

Main Methods:

Inferring gene families and encoded proteins from genomic data.
Applying phylogenomic analyses to these inferred families.
Constructing species trees based on gene family evolution.

Main Results:

Established protocols for gene family inference.
Demonstrated the utility of gene families in phylogenomic analyses.
Successfully inferred species trees using the described methods.

Conclusions:

Minimal protocols enable robust gene family inference.
Gene family analysis is a powerful approach for phylogenomics.
This work facilitates accurate reconstruction of species evolutionary histories.