Analysis 8: Phylogenetic Placement of Bins with PhyloPhlAn - cecilia-andersson/Genome_Analysis_Project GitHub Wiki
It was a bit difficult to get the PhyloPhlAn program to work: some troubleshooting I had to do on my own included manually uploading configuration files to the correct directory, and running the phylophlan_metagenome program a second time because the first did not recognize the database path to identify species.
From the tree, it appears that two bins (43 and 6) are the most closely related, and that there are a few species (33, 1, and 30) which are more distantly related from the majority of organisms in the sample. Hopefully the second run of the classification code works prior to turn-in time, as it would be interesting to see just how different these outliers are from the main branch.
I haven't yet gotten potential taxonomic IDs for the organisms present, but was able to use the .tre file output to understand which of my bins were possibly related to each other:
From the tree, it appears that two bins (43 and 6) are the most closely related, and that there are a few species (33, 1, and 30) which are more distantly related from the majority of organisms in the sample. Hopefully the second run of the classification code works prior to turn-in time, as it would be interesting to see just how different these outliers are from the main branch.