Example sentences for: jtt-f

How can you use “jtt-f” in a sentence? Here are some example sentences to help you improve your vocabulary:

  • In addition, phylogenetic analyses were conducted with maximum likelihood (JTT-F option) [ 31 ] and maximum parsimony (Max-Mini Branch & Bound option) [ 29 ] on combined data sets; in all cases they resulted in similar results (topology and significance) to the neighbor-joining analyses.

  • Shimodaira-Hasegawa tests [ 17 ] were performed in PAML [ 30 ] (JTT-F option, fixed gamma); p-values for each topology were recorded.

  • Pairwise evolutionary distances between the sequences in concatenated alignments were calculated using the Dayhoff PAM model as implemented in the PROTDIST program of the PHYLIP package [ 44 ] . A distance tree was constructed from the resulting distance matrix by using the least-square [ 46 ] method as implemented in the FITCH program of PHYLIP [ 44 ] . The maximum likelihood tree was constructed with the JTT-F model of amino acid substitutions [ 47 ] , as implemented in the ProtML program of the MOLPHY package [ 48 ] , by optimizing the least squares tree with local rearrangements.


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