Abstract. Phylogenetic analysis is an area of computational biology concerned with the reconstruction of evolutionary relationships between organisms, genes, and gene families. Maximum likelihood evaluation has proven to be one of the most reliable methods for constructing phylogenetic trees. The huge computational requirements associated with maximum likelihood analysis means that it is not feasible to produce large phylogenetic trees using a single processor. We have completed a fully cross platform coarse-grained distributed application, DPRml, which overcomes many of the limitations imposed by the current set of parallel phylogenetic programs. We have completed a set of efficiency tests that show how to maximise efficiency while using the program to build large phylogenetic trees. The software is publicly available under the terms of the GNU general public licence from the system webpage at

Lentiviruses are one of several groups of retroviruses. In early studies of the molecular phylogenetic analysis of endogenous and exogenous retroviruses it was suggested that the retroviruses could be divided into four groups, two complex with several accessory or regulatory genes (lentiviruses; and the bovine and primate leukemia virus group now known as deltaretrovirus) and two simple, with

HIV-1 non-subtype B viruses are predominant worldwide. At least 9 different HIV-1 group M subtypes and 14 circulating recombinant forms differ from one another by 10-15 % in their pol gene, which includes the coding regions for the viral protease and reverse transcriptase (RT), the current targets of antiretroviral drugs. Inter-subtype genotypic diversity includes polymorphism at amino acid residues known to be related to drug resistance in HIV-1 subtype B. Whether polymorphism alters protease and RT function, drug susceptibility, or clinical response to treatment, is unclear. Worldwide dissemination of non-subtype B viruses and increasing availability of antiretroviral drugs in the developing world will expand drug use and the likelihood of drug resistance in non-subtype B viruses. In this review we define and characterize inter-subtype RT and protease polymorphism, and examine the evidence for genotypic and phenotypic differences between HIV-1 subtypes as well as the potential for different clinical responses and evolution of drug resistance among non-B infected individuals. Key words HIV-1 subtypes. Polymorphism. Drug resistance.

This is to certify that I have examined this copy of a doctoral dissertation by

The electronic version of this article is the complete one and can be found online at

This is an Open Access article distributed under the terms of the Creative Commons Attribution License

The distribution of CTL epitopes in HIV-1 appears to be random,

of superinfection, strengths and weaknesses of standard resistance assays, treatment interruptions, resistance to new antiretrovirals, and other topics. Sex took center stage at the 2003 Resistance Workshop. And the 200 assembled clinicians and scientists weren’t talking about viral sex—the term Jaap Goudsmit coined for recombination of two HIV strains [1]. They were talking about the real thing, between women and men and between men and men. Introducing perhaps the most important clinical study of the workshop, Michael Kozal (Yale University) inspired the title of this article when he renamed his talk “Sex, drugs, and resistance. ” But his study was only one of many that explored the serpentine links entwining those three high-speed highways. Other researchers posed an important new question about HIV superinfection—Does it happen much more than we think?—while a few teams tracked some discouraging trends in transmission of drug-resistant virus. Clever mathematical modeling suggested how infection with herpes simplex virus type 2 (HSV-2) can speed the spread of drug-resistant HIV, while a clutch of studies underscored the unreliability of some standard resistance assays. The meeting had its share of potentially good news, mostly involving new antiretrovirals or genotyping. And one

Abstract not found

Research article Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans