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Example sentences for: dayhoff

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Phylogenetic trees were constructed by first generating a distance matrix using the PROTDIST program and the Dayhoff PAM model for amino-acid substitutions and employing this matrix for minimum evolution (least-square) tree building [ 30] using the FITCH program.
3. Maximum likelihood pairwise distance matrices are calculated for each of the x multiple alignments using a model of amino acid substitution (for example, BLOSUM [ 25 ] or Dayhoff PAM [ 26 ] ).
The distance matrix was obtained using Protdist with a Dayhoff Pam matrix.
Many proteins belong to large families, as suggested by Dayhoff [ 1 ] . Such families are often composed of subfamilies related to each other by gene duplication events.
Distances between aligned proteins were estimated with the Dayhoff amino-acid replacement model [ 51 ] . Tree topologies were then inferred from these distances via neighbor-joining [ 52 ] and 1,000 non-parametric bootstrap replicates were used to estimate clade support [ 53 ] . Maximum likelihood analysis produced topologies consistent with the neighbor-joining analysis.