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By Allen G. Rodrigo, Gerald H. Learn Jr.

Computational and Evolutionary research of HIV Molecular Sequences is for all researchers attracted to HIV learn, even those that merely have a nodding acquaintance with computational biology (or people who are acquainted with a few, yet no longer all, points of the field). HIV examine is uncommon in that it brings jointly scientists from a variety of disciplines: clinicians, pathologists, immunologists, epidemiologists, virologists, computational biologists, structural biologists, evolutionary biologists, statisticians and mathematicians. This e-book seeks to bridge the space among those teams, in either subject material and terminology. targeted mostly on HIV genetic version, Computational and Evolutionary research of HIV Molecular Sequences covers such matters as sampling and processing sequences, inhabitants genetics, phylogenetics and drug objectives.

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Extra info for Computational and Evolutionary Analysis of HIV Molecular Sequences

Example text

MP is much faster than ML, but still slow compared to most distance-based methods. Both these methods calculate large numbers of trees and compare them by either the likelihood or the parsimony score. , 1994) but for large numbers of sequences the computational burden is still a major hurdle. In this group, Neighbor Joining (NJ) is by far the most popular method. It is very fast and generally quite good, although there are conditions under which it is biased (i. , it systematically produces a wrong tree).

Since we still do not have a full understanding of the origins and relationships of HIV and the subtypes, the timing of HIV's history is made even more difficult. , 1988; Sharp and Li, 1988). Today the common view is that the origin of SIV may date back millions of years, but that the current HIV-1 and HIV-2 epidemics were caused by several more recent introductions of SIV strains into humans. While there has been some debate whether a molecular clock is applicable to HIV or not, it has recently been shown that HIV-1 does evolve in a clock-like fashion (Leitner and Albert, 1999).

1996b). , 1997), but despite extensive searching no parental subtype E or subtype I genome has been found yet. Some recombinants (most notably the MAL isolate) were identified even before the subtypes were introduced. In the 1987 Human retroviruses and AIDS compendium, Myers mentioned that “the MAL genes display a disjunctive pattern of divergence relative to other isolates... A plausible explanation for this effect is that the MAL genome has been involved in recombination with a more divergent virus” (Myers, 1987).

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