Create, Analyze, and Visualize Phylogenomic Datasets Using PhyloFisher-Reference-Cited by-同舟云学术

Create, Analyze, and Visualize Phylogenomic Datasets Using PhyloFisher

Published:2024-01 Issue:1 Volume:4 Page:
ISSN:2691-1299
Container-title:Current Protocols
language:en
Short-container-title:Current Protocols

Author:

Jones Robert E.¹²^ORCID,Tice Alexander K.¹²³^ORCID,Eliáš Marek⁴^ORCID,Eme Laura⁵^ORCID,Kolísko Martin⁶⁷^ORCID,Nenarokov Serafim⁶,Pánek Tomáš⁸^ORCID,Rokas Antonis⁹^ORCID,Salomaki Eric⁶¹⁰^ORCID,Strassert Jürgen F. H.¹¹^ORCID,Shen Xing‐Xing¹²^ORCID,Žihala David⁴^ORCID,Brown Matthew W.¹²^ORCID

Affiliation:

1. Department of Biological Sciences Mississippi State University Starkville Mississippi USA

2. Institute for Genomics, Biocomputing & Biotechnology Mississippi State University Starkville Mississippi USA

3. Department of Biological Sciences Texas Tech University Lubbock Texas USA

4. Department of Biology and Ecology, Faculty of Science University of Ostrava Ostrava Czech Republic

5. Unité d'Ecologie, Systématique et Evolution, CNRS Université Paris‐Saclay France Orsay France

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

7. Faculty of Science University of South Bohemia České Budějovice Czech Republic

8. Department of Zoology, Faculty of Science Charles University Prague Czech Republic

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

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

11. Department of Evolutionary and Integrative Ecology Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany

12. Institute of Insect Sciences Zhejiang University Hangzhou China

Abstract

AbstractPhyloFisher 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 datasetBasic Protocol 2: Performing phylogenomic analysesSupport Protocol 1: Installing PhyloFisherSupport Protocol 2: Creating a custom phylogenomic database

Publisher

Wiley

Link

https://currentprotocols.onlinelibrary.wiley.com/doi/pdf/10.1002/cpz1.969

Reference22 articles.

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