Words similar to phylip

Example sentences for: phylip

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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 resulting datasets were subjected to 1,000 (Clustal) or 100 (Phylip) rounds of bootstrapping [ 66] to evaluate the statistical significance of the consensus tree topologies.
The PROTDIST and FITCH programs are modules of the PHYLIP software package [ 31].
We generated phylogenetic trees using the neighbor-joining algorithm [ 62], as implemented in the two standard phylogenetic analysis software packages, ClustalX [ 63, 64] and Phylip [ 65].
Neighbor-joining (PHYLIP), Fitch and Margolash (Fitch in PHYLIP), and maximum parsimony methods [ 21] all produced trees consistent with one another.