Plasmid phylogenetic profiling

Question

[jeccy.J]

Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using any visualization network can anyone please suggest any tool, where i can visualization in network i have gone though few paper which use cytoscape, any other suggestion also appreciated.

Thank you advance.

Answer 1

[Manvendra Singh]

I recommend using Network 4.6.1.2 which can be downloaded here

It can clearly show your haplotypes in minimum spanning network. A tutorial is also available on the website.

If you just play around, it produces beautiful networks. It is generally used in population genetics.

Have a look on this publication, I had made a network on Mitochondrial sequences.

[jeccy.J]

Thanks for suggestion. Could you please let me know whether I can feed local blast result to the network? I need to do few blast between All vs All and feed the data to network.

[Manvendra Singh]

You would just need to have your file in aligned format, fasta or nexus. Just read it that how it works, then it would be even easier.