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Example sentences for: dayhoff

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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.
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.
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.
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.
The distance matrix was obtained using Protdist with a Dayhoff Pam matrix.