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.
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The latest version of TreeFix-TP can be found here.
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Installation instructions for TreeFix-TP can be found here.
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The manual can be found here, which includes information on requirements which must be installed.
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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.
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A test script which runs TreeFix-TP on example data can be found here.
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We recommend using a maximum likelihood tree generated using RAxML.
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If you have any problems installing or using TreeFix-TP, please submit an issue here or email [email protected].