I am having problems to get the phylogenetic tree at the end of my script.
Even asking in my batch file (MCC) a memory of 500 GB and 128 processors, I am not able to get this file (Mothur crashes). Is there any command to manage this issue?
This is the current command:
How big is final.phylip.dist? How many sequences are in final.fasta?
The reality is that modern datasets have so many sequences that it is hard to get a reasonably sized distance matrix that you can use to build a tree. We use a number of “tricks” to get clustering to work that we can’t do with phylogenetic methods. FWIW, I have yet to run into a case where inferences drawn from Bray-Curtis distances are meaningfully different those using weighted UniFrac. That being said, if your reads don’t fully overlap you might need to see this…