TreeFix-TP

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 (Description from UConn Computational Biology page).

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