Visualising Roary Results

Question

[Fid_o]

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?

Answer 1

[herber4]

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/

[Neel]

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