Monthly Archives: September 2012

Fieldwork!!!!

Saturday is a fieldwork day. I’ll be posting a bunch of stuff up ranging from notebook scans, GIS files, and maps. All will be CCBY and I will attached the license. Site: White Mesa Geologic Overview I am in the … Continue reading

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Code for your geomicrobiology!!!

Finally a post about geomicrobiology. Over on github I set up a repo. Most the codes are not comment and there are no docs as of yet.   One that might interest geomicro folks is some code I wrote that … Continue reading

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Reference Sequences (NCBI)

In my obsession to create a genus level tree I stumbled across the NCBI RefSeq. This is a high quality 16S dataset from NCBI. You can access it from an FTP site or at the search bar. From the NCBI … Continue reading

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Network Analysis of the Cyano Tree

Here is the network analysis of the cyano tree. This 16S alignment was done in muscle. The tree was built using PhyML with 100 bootstraps. The network analysis was carried out in SplitsTree.

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Cyano ML tree

Here is the ML tree for the cyano bacteria by genera with two removed due to bad 16S data.

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