I don't need to go to the species level, just the genus level, and I would like to make a hierarchal taxonomic tree to show from phylum (proteobacteria) down to each genus. My plan is to then point out each genus where my system of interest is found. Does anyone know how to do this? I'm not really a bioinformatics person so I wonder if there is some tool or software I am missing out on. Thank you so much!
Hi,
You can try the Philipp package and bootstrap softwares, they are very simple to work with, also you can find tutorials on line for them. Hope that helps, Regards!
If you need "just the tree", the Living Tree project might contain what you need. It has a PDF with the full tree as well as the NEWICK file. The latter you can then customize with tree viewing tools like iTOL or ARB. The thing is rather unwieldy though, as it is quite big...
http://www.arb-silva.de/projects/living-tree/
What is purpose of the tree? Are you looking to find evolution and distribution of a gene or protein throughout the proteobacterial phyla?
Hi Manan,
I am looking at genes that are horizontally transferred between bacteria and I want to show their distribution throughout proteobacteria. I need this for a figure for a paper.
Thanks!
I will add that a phylogenetic tree would be fine also, but I haven't found any way to interrupt the tree at the genus level rather than going down to each individual species and strain.
Hi April, Below are some URLS that might be helpful.
http://nar.oxfordjournals.org/content/early/2014/04/11/nar.gku241.full
http://www.nature.com/nrmicro/journal/v9/n6/full/nrmicro2577.html
http://www.ncbi.nlm.nih.gov/pubmed/25710183
The problem with a tree if the genera is that not all genera are well defined by, e.g., a 16S-based tree (take Escherichia/Shigella/Salmonella as an obvious example). So you have either mixed groups or a lot of individual entries.
Next problem: The total amount of genera in the Proteobacteria is huge (there are 847 genera in the Living Tree). That would make the Figure basically unreadable (even if you break it down on Alpha-, Beta-, etc.).
How about making the cut on the level of families?
You can construct phylogenetic tree using claustal W or omega. How can get the sequence from ncbi website and do multiple sequence alignment and use it for phylogenetic analysis
Try with: Geneious ( free trial ), mega (free, http://www.megasoftware.net), split tree (free, http://www.splitstree.org), unpro UGENE (free, http://ugene.unipro.ru); most of them have the same algorithm !!
Hello April,
As others have mentioned, you could infer a phylogenetic tree from an aligned matrix of orthologous genes. However, there is a difference between making a tree and making a correct tree.
Your problem is further complicated because there probably is no correct tree for your group of interest. The prevalence of HGT among prokaryotes means that a strictly bifurcating phylogeny is almost certainly not a correct depiction of the evolutionary history of the group: there is no tree, only a reticulation. The softwares mentioned in this thread will happily churn out trees (even highly supported ones) if you give them data. But, they will not consider the possibility of branches merging or crossing, and as such cannot provide you with a correct answer.
Just some food for thought :)
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