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 (v7.1) 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). This version upload consists of:

Alteromonas_Pangenome_v2.md: A reproducible workflow that details the process of making this digital organism, from start to finish.

Alteromonas_genomes_databases_v2.tar.gz: A compressed directory consisting of all contigs databases used to make 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.db.zip: Compressed genomes storage database created in anvi'o from all of the contigs files and external-genomes file.

Alteromonas_Pangenome_2.tar.gz: Compressed file containing the Alteromonas pangenome (digital organism).

misc_Alteromonas_Pangenome_v2.tar.gz: Compressed directory containing any information that anvi'o created when forming the pangenome.

ANI.zip: Compressed directory containing all output files from assessing genome similarity.

*concatenated-proteins.fa: Concatenated core protein files for all three types of core gene sets.

RAxML_bestTree*:  Trees determined for all three sets of core genes from RAxML.

midpoint_mags_*: Midpoint rooted trees for all three sets of core genes.

bayesian_core_gene_list.txt: List of gene cluster ids used to make the phylogeny from the bayesian core.

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