Load the Example Settings and the Data

We start by getting the example difficulty level. If you want to use a different example difficulty level, useparalleldemoconfigand then run this example again. SeeCustomizing the Settings for the Examples in the Parallel Computing Toolbox™for full details.

difficulty = pctdemo_helper_getDefaults();

Thepctdemo_setup_hivfunction retrieves the protein sequence information from the NCBI GenBank® database, and thedifficultyparameter controls how many protein sequences we retrieve. You canview the code for pctdemo_setup_hivfor full details.

[fig, pol, description] = pctdemo_setup_hiv(difficulty); numViruses = length(pol); startTime = clock;

Downloading data from the NCBI GenBank database Finished downloading

Calculate the Distances

We callseqpdistto align the POL sequences and use the Tajima-Nei metric to measure the distances between them.

pold = seqpdist(pol,'method','Tajima-Nei','Alphabet','NT',...'indel','pair');

Measure the Elapsed Time

The time used for the sequential computations should be compared against the time it takes to perform the same set of calculations using the Parallel Computing Toolbox in theDistributed Analysis of the Origin of the Human Immunodeficiency Virusexample. The elapsed time varies with the underlying hardware.

elapsedTime = etime(clock, startTime); fprintf('Elapsed time is %2.1f seconds\n', elapsedTime);

Elapsed time is 12.6 seconds

Plot the Results

Now that we have all the distances, we can construct the phylogenetic tree for the POL proteins. You canview the code for pctdemo_plot_hivfor full details.

pctdemo_plot_hiv(无花果、pold、描述);