Example sentences for: phylip

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

  • Maximum likelihood pairwise distances are calculated using BLOSUM matrices [ 25 ] by a modified version of TREE-PUZZLE [ 34 ] . Neighbor joining trees are calculated by a modified version of NEIGHBOR from the PHYLIP package [ 35 ] http://evolution.genetics.washington.edu/phylip.html.

  • 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.

  • 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].

  • An alignment output from this source was used to create a dendrogram using TreeTop [ 45 ] with PHYLIP output (default parameters) at a node of the European Molecular Biology Network http://www.genebee.msu.su [ 47 ] . Potential phosphorylation sites were identified using NetPhos 2.0 http://www.cbs.dtu.dk/services/NetPhos [ 48 ] . After alignment with CLUSTAL W, identical and similar amino acids in Figure 3were identified using MacBoxshade 2.15 http://www.isrec.isb-sib.ch/ftp-server/boxshade/MacBoxshade.

  • All phylogenetic reconstructions were performed with the PHYLIP and PAML software packages [ 54 55 ] .

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