www.gusucode.com > distcomp 案例源码程序 matlab代码 > distcomp/pctdemo_plot_hiv.m
function pctdemo_plot_hiv(fig, pold, description) %#ok<INUSL> %PCTDEMO_PLOT_HIV Create the graphs for the Parallel Computing Toolbox %Gene Sequence Alignment Example. % pctdemo_plot_hiv(fig, gagd, pold, envd, description) displays the % phylogenetic trees based on the specified distances. % % pold measures the distance between the POL polyprotein sequences. % % description is the virus description obtained from pctdemo_setup_hiv. % Copyright 2007-2012 The MathWorks, Inc. % Phylogenetic tree reconstruction % % The *seqpdist* and *seqlinkage* commands are used to construct a % phylogenetic tree for the POL coding region using the Tajima-Nei % method to measure the distance between the sequences and the % unweighted pair group method using arithmetic averages, or UPGMA % method, for the hierarchical clustering. The Tajima-Nei method is % only defined for nucleotides, therefore nucleotide sequences are used % rather than the translated amino acid sequences. The distance % calculation is very computationally intensive. % % Note: The distance has been calculated in the Parallel Computing % Toolbox Gene Sequence Alignment examples, and is passed as the pold % parameter to this function. % poltree = seqlinkage(pold, 'WPGMA', description); % Calling plot on a phylogenetic tree always opens a new figure, so we % cannot use the input argument fig here. h = plot(poltree, 'type', 'angular'); ax = h.axes; fig = get(ax, 'parent'); set(fig, 'Name', 'Analysis of the Origin of HIV'); title(ax, 'Immunodeficiency virus (POL polyprotein)') xlabel(ax, 'Patristic distance'); % Analyzing the origins of the HIV virus from the plot % % Please note that not all the viruses are used for the computations % at the default difficulty level. If you run this example at a sufficiently % high difficulty level, all the viruses will be included in the % distance calculations and the following discussion applies. % % The phylogenetic tree resulting from our analysis illustrates the % presence of two clusters and some other isolated strains. The most % compact cluster includes all the HIV2 samples; at the top branch of % this cluster we observe the sooty mangabey which has been identified % as the origin of this lentivirus in humans. The cluster containing % the HIV1 strain, however is not as compact as the HIV2 cluster. From % the tree it appears that the Chimpanzee is the source of HIV1, % however, the origin of the cross-species transmission to humans is % still a matter of debate amongst HIV researchers. end % End of pctdemo_plot_hiv.