CAFE 5 models variation in evolutionary rates among gene families
Abstract
Motivation: Genome sequencing projects have revealed frequent gains and losses of genes between species. Previous versions of our software, Computational Analysis of gene Family Evolution (CAFE), have allowed researchers to estimate parameters of gene gain and loss across a phylogenetic tree. However, the underlying model assumed that all gene families had the same rate of evolution, despite evidence suggesting a large amount of variation in rates among families. Results: Here, we present CAFE 5, a completely re-written software package with numerous performance and user-interface enhancements over previous versions. These include improved support for multithreading, the explicit modeling of rate variation among families using gamma-distributed rate categories, and command-line arguments that preclude the use of accessory scripts. Availability and implementation: CAFE 5 source code, documentation, test data and a detailed manual with examples are freely available at https://github.com/hahnlab/CAFE5/releases. Supplementary information: Supplementary data are available at Bioinformatics online.
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Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187 · see citing works
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960 · see citing works
CAFE: a computational tool for the study of gene family evolution
De Bie, T., Cristianini, N., Demuth, J. P., & Hahn, M. W. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl097 · Cited by 1,790 · see citing works
Self-citationComparative Genomics of the Eukaryotes
Rubin, G. M., Yandell, M. D., Wortman, J. R., Gabor, G. L., Miklos, Nelson, C. R., Hariharan, I. K., Fortini, M. E., Li, P. W., Apweiler, R., et al. (2000) · Science · doi:10.1126/science.287.5461.2204 · Cited by 1,698 · see citing works
Evolutionary and biomedical insights from the rhesus macaque genome.
Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., Remington, K. A., Strausberg, R. L., Venter, J. C., Wilson, R. K., et al. (2007) · Science · doi:10.1126/science.1139247 · Cited by 1,403 · see citing works
Self-citationAmong-site rate variation and its impact on phylogenetic analyses
Yang, Z. (1996) · Trends in Ecology & Evolution · doi:10.1016/0169-5347(96)10041-0 · Cited by 1,202 · see citing works
Han, M., Thomas, G. W. C., Lugo-Martinez, J., & Hahn, M. W. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst100 · Cited by 830 · see citing works
Self-citationOrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs
Waterhouse, R. M., Tegenfeldt, F., Li, J., Zdobnov, E. M., & Kriventseva, E. V. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1116 · Cited by 387 · see citing works
The Evolution of Mammalian Gene Families
Demuth, J. P., Bie, T. D., Stajich, J., Cristianini, N., & Hahn, M. W. (2006) · PLoS ONE · doi:10.1371/journal.pone.0000085 · Cited by 376 · see citing works
Self-citationA Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences
Pupko, T., Pe, I., Ron Shamir, A., & Graur, D. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026369 · Cited by 355 · see citing works
Gene Family Evolution across 12 Drosophila Genomes
Hahn, M. W., Han, M., & Han, S.-G. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030197 · Cited by 355 · see citing works
Self-citationEstimating the tempo and mode of gene family evolution from comparative genomic dataPreprint
Hahn, M. W., Bie, T. D., Stajich, J., Nguyen, C., & Cristianini, N. (2005) · Genome Research · doi:10.1101/gr.3567505 · Cited by 319 · see citing works
Self-citationGene content evolution in the arthropods
Thomas, G. W. C., Dohmen, E., Hughes, D., Murali, S. C., Poelchau, M. F., Glastad, K. M., Anstead, C. A., Ayoub, N. A., Batterham, P., Bellair, M., et al. (2020) · Genome biology · doi:10.1186/s13059-019-1925-7 · Cited by 229 · see citing works
Self-citationEstimates of DNA and protein sequence divergence: an examination of some assumptions.
Golding, G. B. (1984) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040303 · Cited by 124 · see citing works
BadiRate: estimating family turnover rates by likelihood-based methods
Librado, P., Vieira, F. G., & Rozas, J. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr623 · Cited by 120 · see citing works
VARIABILITY OF EVOLUTIONARY RATES OF DNA
Gillespie, J. H. (1986) · Genetics · doi:10.1093/genetics/113.4.1077 · Cited by 91 · see citing works
Determining the evolutionary history of gene families
Ames, R. M., Money, D., Ghatge, V. P., Whelan, S., & Lovell, S. C. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr592 · Cited by 42 · see citing works
Prost, S., Armstrong, E. E., Nylander, J. A. A., Thomas, G. W. C., Suh, A., Petersen, B., Dalén, L., Benz, B. W., Blom, M. P. K., Palkopoulou, E., et al. (2019) · GigaScience · doi:10.1093/gigascience/giz003 · Cited by 32 · see citing works
Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques
Thomas, G. W. C., Wang, R. J., Nguyen, J., Harris, R. A., Raveendran, M., Rogers, J., & Hahn, M. W. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa303 · Cited by 21 · see citing works
Self-citationThe nonrandom evolution of gene families
Casola, C., & Lawing, A. M. (2018) · American Journal of Botany · doi:10.1002/ajb2.1211 · Cited by 2 · see citing works
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- Authors
- Mendes, F. K., Vanderpool, D., Fulton, B., & Hahn, M. W.
- Affiliations
- University of Auckland (NZ)
- Indiana University Bloomington (US)
- Corresponding author
- Vanderpool, Dan
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-12-01
- Volume
- 36
- Issue
- 22-23
- Pages
- 5516-5518
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W3113087152
- Semantic Scholar
- bb8eab127370b6056aa95aa15b9c6da78c6940f2
- Cited by
- 833
- References
- 20
- Citations by year
- 2026: 219 · 2025: 237 · 2024: 189 · 2023: 110 · 2022: 58 · 2021: 19
- FWCI
- 15.24
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (DBI-1564611)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- gene family evolution, gene gain and loss, phylogenetic analysis software, multithreading, accessory genes
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