Additions to create-genome-phylogeny

elizabethmcd / metabolisHMM

Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs

GNU General Public License v3.0

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Additions to create-genome-phylogeny #37

Closed elizabethmcd closed 4 years ago

elizabethmcd commented 4 years ago

Integrating putative genome classifications with the Hug 2016 et al. TOL of genomes, highlighting input genomes

Argument to download TOL genomes (bacteria, archaea, eukarya, all or some)
Point to already downloaded TOL genomes directory or custom references directory
Point to input references
Make tree
Highlight with metadata input genome for iTOL to visualize where they fall
Also do this for highlighting on the ribosomal tree if a certain single marker falls anywhere

elizabethmcd commented 4 years ago

Put external data file for TOL accessions on github, read file within metabolisHMM create-genome-phylogeny workflow using urllib2 package to read the file and pass to ncbi-genome-download (which I believe can be used within python as arguments/package as well as the CLI)

elizabethmcd commented 4 years ago

just make this a demo, add arguments for refs vs input and highlight on tree