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Visualising Roary Results

I run roary ( roary -e --mafft -p 32 *.gff) to produce core genome alignment on hundreds of Salmonella sequences and have results. I have the following files in the results:

  1. gene_presence_absence.csv
  2. gene_presence_absence.Rtab
  3. pan_genome_reference.fa
  4. accessory_binary_genes.fa.newick
  5. accessory_graph.dot
  6. core_accessory_graph.dot
  7. core_gene_alignment.aln
  8. clustered_proteins

I would like to visualise the panSNP tree with the roary matrix of these sequences using the command: roary_plots.py name_of_your_newick_tree_file.tre gene_presence_absence.csv. But I realise I have no .tre file in my roary outcome. How do I generate this .tre file from my sequences or from the roary outcome I have?

sequence roary snp genome alignment
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updated by Neel • Neel • written by Fid_o • Fid_o

1 answer

you can use a program like FastTree where you input the core_gene.aln file and it outputs the Newick tree file

fasttree core_gene.aln > tree.file

http://www.microbesonline.org/fasttree/

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written by herber4 • herber4

How to make flower plot from roary output file? Is there anyway to know how many accessory and unique genes each strain has?

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written by Neel • Neel

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