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Example sentences for: dayhoff

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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 ] ).
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.
The distance matrix was obtained using Protdist with a Dayhoff Pam matrix.
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.
For all three possible unrooted tree topologies maximum-likelihood values and posterior probabilities were calculated using in-house JAVA programs that were written utilizing classes from the Phylogenetic Analysis Library version 1.0 [ 54 ] and parts of Vanilla package version 1.0 [ 54 ] . If not indicated otherwise, likelihood values were estimated using the automatically selected suitable substitution model (chosen from BLOSUM62, CPREV, Dayhoff, JTT, MTREV24, VT and WAG) with no ASRV.