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David Coil edited Building a 16S rDNA Phylogenetic Tree.md
almost 10 years ago
Commit id: ff6100fd572b3ff9a5168beb1cc39baa5cea5ba8
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and download the FastTree.c program by right clicking on it and saving the link to your Applications folder. To compile the software, navigate to your Applications folder in a Terminal window:
cd /Applications
Then, type:
gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm
...
gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm
Now, you should have a working version of FastTree. To build your tree, using the cleaned up RDP alignment,
type: type the following (be sure the output name ends in ".tre" to ensure it will be recognized by Dendroscope):
/Applications/FastTree -nt RDP_alignemnt_clean.fa > tree_file.tre
The output name ends in ".tre" to ensure that it will be recognized by Dendroscope.
##Viewing the Tree in Dendroscope
Download and install Dendroscope.
http://ab.inf.uni-tuebingen.de/software/dendroscope/