Microbial Innovations

This repository contains the code, data, and outline for the microbial innovations project.

Project Goals

• Aim 1)

• Aim 2)

• Aim 3)

Repo Contents

• bin: *

• data:

  • readme_LTPs123.pdf: Silva Living Tree Project release information
  • fasta_LTP123.eft: Silva Living Tree Project export filter
  • LTPs123_SSU_tree.newick: Silva Living Tree Project tree in Newick format
  • LTPs123_SSU.aligned.fasta Silva Living Tree Project SSU rRNA alignment
  • LTPs123_SSU.arb: Silva Living Tree Project Arb Database
  • nmicrobiol201648-s4.txt: Accession numbers for genomes used in Hug et al 2016
  • nmicrobiol201648-s5.txt: Concatenated ribosomal protein alignment from Hug et al 2016
  • nmicrobiol201648-s6.txt: Maximum likelihood tree (Newick) based on concatenated ribosomal protein alignment from Hug et al 2016
  • nmicrobiol201648-s7.txt: SSU rRNA alignment from Hug et al 2016
  • nmicrobiol201648-s8.txt: Maximum likelihood tree (Newick) based on SSU rRNA alignment from Hug et al 2016.
  • rdp_download_9752seqs.fa: RDP reference FASTA dataset with Type stains from cultured and uncultured sources with size > 1200 bp and good quality (25 Aug 2016)
  • rdp_download_9752seqs.tree: RDP reference tree (ARB compatible) dataset with Type stains from cultured and uncultured sources with size > 1200 bp and good quality (25 Aug 2016)