PhyloFisher is a software package written primarily in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of protein sequences from eukaryotic organisms. Unlike many existing phylogenomic pipelines, PhyloFisher comes with a manually curated database of 240 protein-coding genes, a subset of a previous phylogenetic dataset sampled from 304 eukaryotic taxa. The software package can also utilize a user-created database of eukaryotic proteins, which may be more appropriate for shallow evolutionary questions. PhyloFisher is also equipped with a set of utilities to aid in running routine analyses, such as the prediction of alternative genetic codes, removal of genes and/or taxa based on occupancy/completeness of the dataset, testing for amino acid compositional heterogeneity among sequences, removal of heterotachious and/or fast-evolving sites, removal of fast-evolving taxa, supermatrix creation from randomly resampled genes, and supermatrix creation from nucleotide sequences. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Constructing a phylogenomic dataset Basic Protocol 2: Performing phylogenomic analyses Support Protocol 1: Installing PhyloFisher Support Protocol 2: Creating a custom phylogenomic database.

Center for Computational Biology of Human Disease and Center for Computation and Visualization Brown University Providence Rhode Island USA

Department of Biological Sciences and Evolutionary Studies Initiative Vanderbilt University Nashville Tennessee USA

Department of Biological Sciences Mississippi State University Starkville Mississippi USA

Department of Biological Sciences Texas Tech University Lubbock Texas USA

Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic

Department of Evolutionary and Integrative Ecology Leibniz Institute of Freshwater Ecology and Inland Fisheries Berlin Germany

Department of Zoology Faculty of Science Charles University Prague Czech Republic

Faculty of Science University of South Bohemia České Budějovice Czech Republic

Institute for Genomics Biocomputing and Biotechnology Mississippi State University Starkville Mississippi USA

Institute of Insect Sciences Zhejiang University Hangzhou China

Institute of Parasitology Biology Centre Czech Academy of Sciences České Budějovice Czech Republic USA

Unité d'Ecologie Systématique et Evolution CNRS Université Paris Saclay France Orsay France

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https://thebrownlab.github.io/phylofisher-pages/ - The most up-to-date documentation can be found here, the PhyloFisher GitHub Pages website.