search

jameshadfield / phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny
http://phandango.net
MIT License
113 stars 27 forks source link

data cannot be displayed? #124

Open korinalb opened 6 years ago

korinalb commented 6 years ago

I'm using the gene_presence_absence.csv output from Roary.

When I upload my file, I get an error saying "heads up, blocks provided without a tree, so this data cannot be displayed". How can I fix this?

Thanks!

jameshadfield commented 6 years ago

Hi @korinalb - phandango needs a tree to work (https://github.com/jameshadfield/phandango/wiki/Input%20data%20formats#phylogenies-trees), even with ROARY data - if you drag on a newick tree with the ROARY csv file things should work. If you don't have a tree you could just fake a newick tree with a huge polytomy at the root containing all your taxa i think

peterjc commented 3 years ago

So the expected usage is to drag accessory_binary_genes.fa.newick and accessory_binary_genes.fa.newick from the default Roary output into the browser?

If so, do you want us to clarify the Wiki documentation here: https://github.com/jameshadfield/phandango/wiki/Input%20data%20formats#roary-pan-genome