Phylogenetic Tree Building from BLAST to TreeVIEW

BLAST searching

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The process for building a tree. Note there's an optional third argument, mock, to sidestep the BLAST searches, which take long and have a delay built into them. Here it is, needs to be executed from the directory where fastBLAST.py occurs, and directory name is the path to a directory that will be created by fastBLAST:

home\directory> > python fastBLAST.py queryList.csv directoryName

Alignment

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From here we need to take the result in directoryName\master.txt and run it through alignment and trimming algorithm. To do this use the following command (also from the main scripts directory as fastBLAST.py):

home\directory> python align.py directoryName

Tree building

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Then take the output from the aligning and trimming process and feed it to RAxML. For now I'm using the web applet here. Use the following citation:

A. Stamatakis, P. Hoover, J. Rougemont. A Rapid Bootstrap Algorithm for the RAxML Web-Servers, Systematic Biology, 75(5): 758-771, 2008