I have a question about FastTree method. Thank you.

[yhuang816]

Hi Qiimers, 

I have used FastTree in the QIIME pipeline to build a 16S rRNA phylogenetic tree. The DNA was extracted from municicpal wastewater samples and the sequencing technique is Illumina MiSeq method. 

When I checked the FastTree method description in their link (http://www.microbesonline.org/fasttree/), it is said that "To account for the varying rates of evolution across sites, FastTree uses a single rate for each site (the "CAT" approximation)." My question is what do "sites" mean? or which "sites" they refer to? Do they mean nucleotide sites in the DNA sequences multiple alignments? 

Could anyone help me interpret this please? 

Thank you 

Yannan 

[justink]

Yep, I'm fairly sure they're referring to nucleotide positions along the DNA. 

[yhuang816]

Ok, I get it. Thank you.