- Evolutionary distances for protein-coding sequences: modeling site-specific residue frequenciesA L Halpern
Los Alamos National Laboratory, New Mexico, USA
Mol Biol Evol 15:910-7. 1998..Site-to-site differences in rates, as well as synonymous/nonsynonymous and first/second/third-codon-position differences, arise as a natural consequence of the site-to-site differences in amino acid frequencies...
- Minimally selected p and other tests for a single abrupt changepoint in a binary sequenceA L Halpern
Department of Molecular Genetics and Microbiology, Health Sciences Center, University of New Mexico, Albuquerque 87131, USA
Biometrics 55:1044-50. 1999..The test is compared to the Kolmogorov-Smirnov two-sample test, the maximally selected chi-square, and a likelihood ratio test. The tests are applied to assessing recombination in genetic sequences of HIV...
- Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstructionW J Bruno
Los Alamos National Laboratory, New Mexico 87545, USA
Mol Biol Evol 17:189-97. 2000..Weighbor appears to be relatively immune to the "long branches attract" and "long branch distracts" drawbacks observed with neighbor joining, BIONJ, and parsimony...
- Multiple-changepoint testing for an alternating segments model of a binary sequenceA L Halpern
Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque 87131, USA
Biometrics 56:903-8. 2000..A sample application, the assessment of the possibility of genetic recombination in HIV sequences, is presented...