TreeFix-TP is a program for reconstructing highly accurate infectious disease phylogenetic trees. TreeFix-TP incorporates host information with sequence data to reconstruct the tree using a mixed maximum likelihood / maximum parsimony framework. Given a maximum likelihood phylogeny and a multiple sequence alignment, TreeFix-TP searches among multiple topologies which are supported equally by sequence data (using the Shimodaiara-Hasegawa test statistic). The selected topology is the one that minimizes the number of necessary transmissions.

The input for TreeFix-TP is a multiple sequence alignment in .fasta format, and a maximum likelihood tree in .newick format.

• The latest version of TreeFix-TP can be found here.

• Installation instructions for TreeFix-TP can be found here.

• The manual can be found here, which includes information on requirements which must be installed.

• TreeFix-TP is described in 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. A previous version of the manuscript appeared on bioRxiv.

• A test script which runs TreeFix-TP on example data can be found here.

• We recommend using a maximum likelihood tree generated using RAxML.

• If you have any problems installing or using TreeFix-TP, please submit an issue here or email mukul.bansal@uconn.edu.