Compute capabilities

• beagle (beagle.darwinproject.mit.edu): Obsolescent.
• coyote (coyote.mit.edu): We'll have 50 TB soon!

There are also older, Alm-specific machines that might be reorganized in the coming months.

• nostoc (nostoc.mit.edu, almlab.mit.edu): Runs the lab website, AdaptML, and AnGST front-ends
• pylori: AdaptML and AnGST backends
• vulgaris
• subtilis

Codebase

• Scott (swo)
  • sycamore (github.com/almlab/sycamore): Strips the Greengenes tree files to make Newick trees.
• Lawrence
  • AnGST
  • AdaptML
• Albert
  • Tree.py
  • LeafStripper
• Chris Smillie
  • SLiME
• Jonathan (yonatanf)
  • SparCC: a tool for computing correlations in compositional data, such as 16S surveys.
    • Note: While this standalone version of sparcc is easier to install/use, I'd recommend using the newer version available through PySurvey.
  • PySurvey: a general-utility package designed for performing interactive analysis of (genomic) survey data.
  • strainFinder: a python package for inferring the number and relative-abundances strains from allele frequencies observed in metagenomic data.