Phylograd: fast column-specific calculation of substitution model gradients
Depending on the tree size, PhyloGrad is 30-100 times faster than automatic differentiation in Pytorch and uses 10-100 times less memory. Even in the task of fitting one global model it is still at least 10 times faster than IQ-TREE3. PhyloGrad accelerates current model optimizations and enables the field to easily explore and implement novel site-specific models.
Authors
- Johannes Söding (ORCID: https://orcid.org/0000-0001-9642-8244)
- Benjamin Lieser
- Georgy Belousov
Institutions
- Max Planck Institute for Solar System Research (DE)
- Max Planck Institute for Biophysical Chemistry (DE)
- Max Planck Institute of Experimental Medicine (DE)
- University of Göttingen (DE)
Publication Details
- Journal
- BMC Bioinformatics
- Published
- 2025-12-23
- DOI
- https://doi.org/10.1186/s12859-025-06353-4
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00