PsiPartition: Improved Site Partitioning for Genomic Data by Parameterized Sorting Indices and Bayesian Optimization

PsiPartition is a phylogenetic tool using Bayesian optimization to obtain more accurate reconstructions, especially for large genomic data with more site heterogeneity. It is designed with a parameterized sorting index which can be used to partition sites into different categories. Partitioned models in main-stream phylogenetic software can be used to analyze the categories. [GitHub | Paper]

• Please prepare your sequence alignment in FASTA format. UniProt and COBALT are very good websites.

References

Users are kindly requested to utilize the following citation when referencing this method:

• Xu, Shijie, and Akira Onoda. "PsiPartition: Improved Site Partitioning for Genomic Data by Parameterized Sorting Indices and Bayesian Optimization." bioRxiv (2024): 2024-04.

Please contact shijie.xu@ees.hokudai.ac.jp for any questions.

Changelogs

• 2024/08/08: First release.