TreeFix-TP is a program for reconstructing highly accurate transmission phylogenies, i.e., phylogenies depicting the evolutionary relationships between infectious disease strains (viral or bacterial) transmitted between different hosts. TreeFix-TP is designed for scenarios where multiple strain sequences have been sampled from each infected host, and it uses the host assignment of each sequence sample to error-correct a given maximum likelihood phylogeny of the strain sequences. Specifically, given a maximum likelihood phylogeny, the multiple sequence alignment on which the phylogeny was built, and the host assignment for each sequence, TreeFix-TP searches around the maximum likelihood phylogeny to find an alternate error-corrected phylogeny which is equally well-supported by the sequence data and minimizes the number of necessary inter-host transmissions.
TreeFix-TP is built upon the open-source TreeFix/TreeFix-DTL framework. It is available open source under the GNU general public license.
- Manual: TreeFixTP-Manual.pdf
- Source code and installation instructions: https://github.com/samsledje/TreeFix-TP (available open source under GNU GPL)
TreeFix-TP can be cited as follows:
- TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference
Samuel Sledzieski, Chengchen Zhang, Ion Mandoiu, and Mukul S. Bansal
Pacific Symposium on Biocomputing (PSB) 2021: Proceedings, pages 119-130.
Funding: Development of the software resource(s) available from this webpage was funded in part by U.S. National Science Foundation award CCF 1618347.