This is a good question for the phylogenetic placement Google group which is monitored by the pplacer and epa-ng developers. Note that pplacer is not under active development, you should be using epa-ng. I’m not very familiar with iTOL, but it sounds like you might be misinterpreting the use of the fat format trees. You won’t be able to search for individual reads on that tree, but you can parse the jplace file for this information.

I have the same problems, any suggestions?
In advance thank for your help
Fra

This is a great tutorial. I have followed it through and have been reading the pplacer document along side. I am confused about one thing. I view the output from pplacer in iTOL and I cannot find my query sequences in there. The CSV file shows the edge number but how can I search them in the tree. If i search them with their names the search returns zero.

Please help

I’ve never tried that, so long as it was structured the same way I don’t know why you couldn’t do that. Give it a try with a small test database. You might consider posting your query on the pplacer Google Group to see what Matsen et al. have to say.

thanks in advance

laura

Nothing much to suggest there, you’re interpreting the meaning of edge width correctly. Seems that something funny is going on…

Thanks Jeff! I’m noticing that the edge that appears to have the most reads (i.e. the widest) after using guppy fat and visualizing the tree with Archaeopteryx , is an edge that only has one query sequence placed on it according to the guppy_to_csv file (as opposed to other edges which have 2-8 sequences). Do you have any ideas as to why this might be the case, or am I misunderstanding the function of guppy fat? Your help is very much appreciated!

The csv file created by guppy_to_csv should tell you just that. Just look for the edge_num column.