Thanks very much Guillaume.
It took me a while to run Phyloshift in all mode for all 190 of my metagenome-derived genomes, so I'm sorry I didn't reply earlier. Now that's finished though, I have another problem! I think I successfully merged my .jplace files using the command:
guppy merge Sample_*-bin.*.fa/treeDir/concat.updated.1.jplace -o MergedAll.jplace
guppy merge Sample_9-bin.85.fa/treeDir/concat.updated.1.jplace Sample_9-bin.8.fa/treeDir/concat.updated.1.jplace -o testMerge.jplace
guppy sing -out-dir MergedTrees/ testMerge.jplace
I then opened this in Archaeopteryx and have a total of 12 trees! I assume these are for different markers(?) but I don't understand why, as I thought the marker genes were stuck together - presumably I'm wrong. Anyway, the trees are huge and human-unreadable at the moment so I tried to search for my genome names in Archaeopteryx without any luck. I noticed in the Phylosift documentation that a link to Archaeopteryx instructions is provided (http://www.phylosoft.org/archaeopteryx/
), but the link doesn't work...... Does anyone have a copy of this document (if it's a pdf or similar)?
In summary (sorry this is so long!), I guess what I wanted to know is:
Is a tree generated by the guppy sing command the best way to see where my genome bins sit phylogenetically? If not, can anyone recommend a better method?
Can you tell me why I get so many trees with the sing command? Am I doing something wrong?
Are you able to send me instructions, a tutorial or something similar which has been used in the past to get phylogenetic trees for multiple metagenome-derived genomes? I'm trying to cobble together information from multiple documents but it doesn't appear to be working well and I assume numerous people have done this before.
I'm sorry this is such a long post - thanks so much for your time, and any help you're able to give me.