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HIV evolutionary dynamics within and among hosts.
Lemey P, Rambaut A, Pybus OG. Lemey P, et al. AIDS Rev. 2006 Jul-Sep;8(3):125-40. AIDS Rev. 2006. PMID: 17078483 Review.
The HIV evolutionary processes continuously unfold, leaving a measurable footprint in viral gene sequences. A variety of statistical models and inference techniques have been developed to reconstruct the HIV evolutionary history and to investigate the population gen …
The HIV evolutionary processes continuously unfold, leaving a measurable footprint in viral gene sequences. A variety of stati …
Inferring population history from molecular phylogenies.
Nee S, Holmes EC, Rambaut A, Harvey PH. Nee S, et al. Philos Trans R Soc Lond B Biol Sci. 1995 Jul 29;349(1327):25-31. doi: 10.1098/rstb.1995.0087. Philos Trans R Soc Lond B Biol Sci. 1995. PMID: 8748016
Variable molecular sequences sampled from a population can be used to infer its dynamic history. Graphical methods are developed and applied to real data, illustrating ways of navigating through hypothesis space with two landmarks for reference: constant population size an …
Variable molecular sequences sampled from a population can be used to infer its dynamic history. Graphical methods are developed and …
Revealing the history of infectious disease epidemics through phylogenetic trees.
Holmes EC, Nee S, Rambaut A, Garnett GP, Harvey PH. Holmes EC, et al. Philos Trans R Soc Lond B Biol Sci. 1995 Jul 29;349(1327):33-40. doi: 10.1098/rstb.1995.0088. Philos Trans R Soc Lond B Biol Sci. 1995. PMID: 8748017
A possible reason for the difference is that HCV has coexisted longer with human populations....
A possible reason for the difference is that HCV has coexisted longer with human populations....
Recombination between sequences of hepatitis B virus from different genotypes.
Bollyky PL, Rambaut A, Harvey PH, Holmes EC. Bollyky PL, et al. J Mol Evol. 1996 Feb;42(2):97-102. doi: 10.1007/BF02198834. J Mol Evol. 1996. PMID: 8919861
A comparison of 25 hepatitis B virus (HBV) isolates for which complete genome sequences are available revealed two that occupied different positions in phylogenetic trees reconstructed from different open reading frames. ...A search of the sequence databases showed
A comparison of 25 hepatitis B virus (HBV) isolates for which complete genome sequences are available revealed two that occupied diff
Inferring the population history of an epidemic from a phylogenetic tree.
Ong CK, Nee S, Rambaut A, Harvey PH. Ong CK, et al. J Theor Biol. 1996 Sep 21;182(2):173-8. doi: 10.1006/jtbi.1996.0152. J Theor Biol. 1996. PMID: 8944148
Phylogenetic or family trees reconstructed from a sample of individuals belonging to a population or species can be used to infer population dynamic history. ...When the transformation does fail, the resultant lineages-through-time plot is very similar to a t …
Phylogenetic or family trees reconstructed from a sample of individuals belonging to a population or species can be used to in …
Determinants of rate variation in mammalian DNA sequence evolution.
Bromham L, Rambaut A, Harvey PH. Bromham L, et al. J Mol Evol. 1996 Dec;43(6):610-21. doi: 10.1007/BF02202109. J Mol Evol. 1996. PMID: 8995058
In addition, there is a relationship between the rate of molecular evolution and body size for two nuclear-encoded sequences. ...
In addition, there is a relationship between the rate of molecular evolution and body size for two nuclear-encoded sequences. ...
Bi-De: an application for simulating phylogenetic processes.
Rambaut A, Grassly NC, Nee S, Harvey PH. Rambaut A, et al. Comput Appl Biosci. 1996 Dec;12(6):469-71. doi: 10.1093/bioinformatics/12.6.469. Comput Appl Biosci. 1996. PMID: 9021264
The user may define a constant birth rate and death rate or a function describing how these rates vary by time or population size. ...The package allows the tree produced to be used as a template for the simulated evolution of molecular sequence data under …
The user may define a constant birth rate and death rate or a function describing how these rates vary by time or population s …
Elucidating the population histories and transmission dynamics of papillomaviruses using phylogenetic trees.
Ong CK, Nee S, Rambaut A, Bernard HU, Harvey PH. Ong CK, et al. J Mol Evol. 1997 Feb;44(2):199-206. doi: 10.1007/pl00006136. J Mol Evol. 1997. PMID: 9069180
The results indicate increases in PV populations of both supergroups A and B in the recent past. This form of the increases, which fit a null model of population growth with an exponent increasing in time, is compatible with the fact that human populations have grow …
The results indicate increases in PV populations of both supergroups A and B in the recent past. This form of the increases, which fi …
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees.
Rambaut A, Grassly NC. Rambaut A, et al. Comput Appl Biosci. 1997 Jun;13(3):235-8. doi: 10.1093/bioinformatics/13.3.235. Comput Appl Biosci. 1997. PMID: 9183526
MOTIVATION: Seq-Gen is a program that will simulate the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. Nuc …
MOTIVATION: Seq-Gen is a program that will simulate the evolution of nucleotide sequences along a phylogeny, using common mode …
End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences.
Rambaut A, Harvey PH, Nee S. Rambaut A, et al. Comput Appl Biosci. 1997 Jun;13(3):303-6. doi: 10.1093/bioinformatics/13.3.303. Comput Appl Biosci. 1997. PMID: 9183536
Here we describe a computer package (End-Epi) that uses graphical methods to allow researchers to make inferences about these processes from their data. ...This file contains the compiled application, the manual and a test tree....
Here we describe a computer package (End-Epi) that uses graphical methods to allow researchers to make inferences about these process …
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