Roadmap to the study of gene and protein phylogeny and evolution—A practical guide

Summary, in English

Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionised studies of biodiversity and organismal evolution. This accumulation of data has been paralleled by the creation of numerous public biological databases through which the scientific community can mine the sequences and annotations of genomes, transcriptomes, and proteomes of multiple species. However, to find the appropriate databases and bioinformatic tools for respective inquiries and aims can be challenging. Here, we present a compilation of DNA and protein databases, as well as bioinformatic tools for phylogenetic reconstruction and a wide range of studies on molecular evolution. We provide a protocol for information extraction from biological databases and simple phylogenetic reconstruction using probabilistic and distance methods, facilitating the study of biodiversity and evolution at the molecular level for the broad scientific community.

• Author: Florian Jacques; Paulina Bolivar; Kristian Pietras; Emma U. Hammarlund
• Department/s: Molecular Evolution; LUCC: Lund University Cancer Centre; Experimental oncology; Division of Translational Cancer Research; EpiHealth: Epidemiology for Health; StemTherapy: National Initiative on Stem Cells for Regenerative Therapy
• Publishing year: 2023
• Language: English
• Publication/Series: PLoS ONE
• Volume: 18
• Issue: 2
• Links: http://dx.doi.org/10.1371/journal.pone.0279597
• Document type: Journal article
• Publisher: Public Library of Science (PLoS)
• Topic: Bioinformatics and Systems Biology; Other Medical Sciences not elsewhere specified
• Status: Published
• Research group: Molecular Evolution; Experimental oncology
• ISBN/ISSN/Other: ISSN: 1932-6203