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http://compbio.mit.edu/treefix/tutorial.html
TreeFix-DTL should require about three hours to execute on the dataset above. The reconstructed gene tree will be available in the folder ~/TreeFix-DTL/treefixDTL-1.0.1/examples/sim/G1/ as the file "G1.pep.raxml.treefixDTL.tree".
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https://www.treefix.com.au/contact_us
Contact TreeFix on the Sunshine Coast to speak with a friendly expert. Our goal is to answer all enquiries within 24 hours or less. If for some reason you do no receive a reply within this time frame, or you would like an immediate answer, please call us on 0439 724 013.
https://www.cs.hmc.edu/~yjw/software/treefix/
TreeFix is a phylogenetic method for improving gene tree reconstructions using a test statistic for likelihood equivalence and a species tree aware (reconciliation) cost function. The default TreeFix package is meant for use in eukaryotic genomes. For prokaryotes, use TreeFix-DTL.
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