Hi,

I am trying to get orthology using Synergy2, which in turn needs tree made from Amphora2.

I am not sure how to produce the tree from Amphora output. The output is said to be in phylip format, but the Treeview or quicktree can't read it. Is it because it doesn't have the nested brackets? If so ,what format is this, and what tool can I use to view it?

Query   Marker  Superkingdom    Phylum  Class   Order   Family  Genus   Species
C341382_2   dnaG    Bacteria(1.00)  Firmicutes(1.00)    Bacilli(1.00)   Lactobacillales(1.00)   Streptococcaceae(1.00)  Streptococcus(1.00) Streptococcus pneumoniae(1.00)
C342110_2   dnaG    Bacteria(0.99)  Firmicutes(0.99)    Bacilli(0.99)   Lactobacillales(0.99)   Streptococcaceae(0.99)  Streptococcus(0.99) Streptococcus pneumoniae(0.44)

Also Synergy2 has a few scripts for Amphora, but with very very poor documentation.

I wonder if anybody here has experience with Synergy2 and Amphora2?

My broad aim is to perform comparative genomics amidst related strains. (Aside, when I tried orthomcl, I got an empty orthologs file with all data in inparalogs file, despite adding an outgroup. I have posted that query separately in Biostars, and am awaiting someone to help me with both these tools. )

Thanks much in advance.