This page is an evolving resource for my lab group and anyone else interested in marine microbiology.


Analytical Labs:

UMCES CASIF Stable Isotope Facility

UC Davis Stable Isotope Facility, Analytical Services

Bioinformatics Links:

Intro to perl and Unix for biologists

Another Unix tutorial

R and Bioconductor Manual

JGI’s IMG Database

iMicrobe – where most of CAMERA ended up

MAFFT – command line program for multiple sequence alignment

AliView – current favorite free alignment editor for Mac. can be configured to kick output directly to FastTree and FigTree

FastTree – fast ML trees. But see also.

FigTree – phylogenetic tree viewer

Mauve – genome alignment

mothur – analysis of 16S rRNA amplicon data, among other things

Other Useful Data Sources:

BCO-DMO – Repository for NSF funded Biological and Chemical Oceanography data

eWOCE – World Ocean Circulation Experiment data





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