How to generate a family level phylogeny?

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5.3 years ago

zoe.meziere ▴ 10

Hi all,

I want to generate a 16S family level phylogenetic tree of a bacteria family, and include on the sequence I have to see where it falls within the family. I know the SILVA database has a lot of 16S sequences, that I downloaded. But making a tree out of all those sequences requires much space, that my laptop doesn't have. Also I don't need thousands of sequences. Just enough to have representative sequences to cover the whole family.

So how should I go about this?

Thanks in advance :)

phylogeny 16S • 1.2k views

ADD COMMENT • link 5.3 years ago by zoe.meziere ▴ 10

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Do you have any access to hardware with more power than your laptop?

ADD REPLY • link 5.3 years ago by Joe 21k

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Check out those cloud services such as aws(amazon web services). You pay for it base on your demand. A 16g memory for 5 hours only takes you around $20. Plus, have you checked the qiime2's phylogenic tree function? That actually doesn't use a ton of resources.

ADD REPLY • link 5.3 years ago by zhuchcn • 0

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