Populating phylogenetic tree with multiple draft genomes

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brodie.s...@students.mq.edu.au

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Jun 16, 2018, 10:58:13 PM6/16/18
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Hi Guys,

I'm able to get phylogenetic trees of my individual draft genomes (using the phylosift all mode). I'm also able to make a phylogenetic tree comparing my draft genomes to one another by concatenating the alignment files from each draft genome (as per the tutorial at: http://darlinglab.org/tutorials/marker_phylogeny/). However, in the first instance the tree has references from the marker DB in it, but only one draft genome - and in the later, the tree has multiple draft genomes but no references. Does anyone know how to make a single tree with references AND multiple draft genomes in it?

Any help you can offer would be greatly appreciated.

Brodie

Guillaume Jospin

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Jun 17, 2018, 12:36:06 AM6/17/18
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You can use the guppy merge command on the <samplename>.jplace files (not sure of the exact name here) 

Once your jplace files have been merged you can use another guppy command to view the tree. Probably similar to what you have been doing already. 

I hope this helps. 

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brodie.s...@students.mq.edu.au

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Jun 24, 2018, 4:17:44 AM6/24/18
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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

According to the documentation (https://phylosift.wordpress.com/tutorials/running-phylosift/illumina-tutorial/) the guppy sing command makes some pretty big tree files so I ran it on a test file I made which included just two of my genome bins:

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.

Brodie
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