Alteromonas Digital Organism Databases

This is the home of the database for the Alteromonas Digital Organism, one of C-CoMP's collaborative efforts. This database was created in anvi'o (anvio-dev) primarily by Michelle DeMers (Massachusetts Institute of Technology) and Rogier Braakman (Massachusetts Institute of Technology), with significant help from members of the Meren Lab (A. Murat Eren, Iva Veseli, and Matthew Schechter) and Moran Lab (Zac Cooper and Mary Ann Moran). This version upload consists of:

Alteromonas_Pangenome_v2_1.md: A reproducible workflow that details the additions made to this version of the pangenome from v2.0.0.

MAG31.db, MAG10_FICUS.db, and GCF_903772925.1.db: Three new contigs databases added to the digital organism.

external-genomes-v2.txt: Text file consisting of a list of the genomes used in this digital organism with ID, strain, and source information.

Alteromonas-v2-GENOMES.tar.gz: Compressed genomes storage database created in anvi'o from all of the contigs files and external-genomes file.

Alteromonas_Pangenome_2_1-PAN.db.tar.gz: Compressed file containing the Alteromonas pangenome (digital organism).

Alteromonas_Pangenome_2_1_miscFiles.tar.gz: Compressed directory containing any information that anvi'o created when forming the pangenome.

ANI_2_1.tar.gz: Compressed directory containing all output files from assessing genome similarity.

bayesian_2_1_concatenated_proteins*: Concatenated core protein files made from bayesian core gene sets.

RAxML_*boots:  New RAxML tree artifacts produced for this version of the pangenome, with bootstrap values. Includes midpoint rooted tree.

layer_orders.txt: Tab-delimited file used to import newick tree into the pangenome.

view.txt: Tab-delimited file containing isolate and strain names.