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.
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.
The refined multiple alignment was used as input for generation of a phylogenetic tree using the program package PHYLIP [ 53].
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].
The alignment in Phylip format of the original sequences, before any manual adjustments were made