Words similar to protml
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Example sentences for: protml
How can you use “protml” in a sentence? Here are some example sentences to help you improve your vocabulary:
Alternative topologies were compared either directly, using the ProtML program, or were subjected to local rearrangement first.
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.
The statistical significance of various nodes of this ML tree was assessed using the relative estimate of logarithmic likelihood bootstrap (Protml RELL-BP) with 10,000 replicates.
Briefly, this process involved the construction of a least-squares tree using the FITCH program or a neighbor-joining tree using the NEIGHBOR program (both from the Phylip package) [ 38], followed by local rearrangement using the Protml program of the Molphy package [ 37] to arrive at the maximum likelihood (ML) tree.
Alternative topologies were created manually by modifications of the original tree and directly compared by ProtML.
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