ArticlePloS one2023
Roadmap to the study of gene and protein phylogeny and evolution-A practical guide.
Article in PloS one, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Pathogenic bacterial profile and antimicrobial susceptibility patterns in odontogenic facial cellulitis among Egyptian patients: A cross-sectional study.Scientific reports · 2026Article
- Protein Language Models: Applications and Perspectives.Journal of proteome research · 2026Review
- Differential expression of reproduction and sex-determining genes in the gonads of genotypic and temperature-induced males of gibel carp (Carassius gibelio).Scientific reports · 2025Article
- A framework for identifying and prioritizing SNPs in genes of the hypothalamic- pituitary-gonadal axis in Guzerat cattle using amplicon-based NGS.BMC genomic data · 2025Article
- Genome-wide identification and characterization of the universal stress protein (USP) gene family in the AC genome of Brassica species.Genetica · 2025Article
- Enhancing nucleotide sequence representations in genomic analysis with contrastive optimization.Communications biology · 2025Article
- A non-hypothesis-driven practical laboratory activity on functional metagenomics: "fishing" protein-coding DNA sequences from microbiomes.Frontiers in bioengineering and biotechnology · 2025Article
- Characterization and organization of telomeric-linked helicase (tlh) gene families in Fusarium oxysporum.Current genetics · 2024Article
- THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis.Genome biology and evolution · 2024Article
- Structural Phylogenetics with Protein Mass Spectrometry: A Proof-of-Concept.The protein journal · 2024Article
- Protein homeostasis imprinting across evolution.NAR genomics and bioinformatics · 2024Article
- Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea.Genes · 2023Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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