Hello,
I am trying to create a phylogenetic tree using my single protein sequence. I know that phylogeny.fr pulls from other databases to create a tree but does anyone know of other software? I feel as though it is an incomplete tree.
Thanks
Hi Sarah,
would you like to elaborate your question? Several softwares can build phylogenetic trees based on protein sequences. I'm wondering if what you want is to access a database from where you can download more sequences from other organisms?
As mentioned above, MEGA might be a good option if you already have your whole dataset, and especially if you are not familiar with other phylogenetic softwares. It is quite user-friendly, and you can do basic things like model-selection and NJ or ML reconstructions.
Good luck!
single sequence phylogenetic tree will be of no use and also not possible. phylogentics represents the evolutionary relation among the multiple sequence. yes it is possible that you go will same sequence from different organisms.
Sorry. Allow me to elaborate. We have recently published a paper entitled "CpaA a Novel Protease from Acinetobacter baumannii Clinical Isolates Deregulates Blood Coagulation." In FEMS Microbiology Letters. I wanted to build a phylogenetic tree based on the sequence we publised within that journal. I would like to be able to just input our sequence and have it pull similar sequences to build the tree. Does that help or have I made it more convoluted?
It seems you need to find homologous (related) sequences for your protein as a first step, and then build your phylogeny. I am not aware of an online tool that does both in one step (as a 'black box').
The standard way is to use BLAST (http://blast.st-va.ncbi.nlm.nih.gov/Blast.cgi) to search for related(homologous) sequences, which requires some bioinformatics skills. One of the multiple issues with homology search for a novel protein like yours is that there might not be many close protein sequences and you may have to look for distant homologs (e.g. as HMMER can do http://hmmer.janelia.org/).
For people with limited comp. bio. background, however, MEGA / Geneous (http://www.geneious.com/features) are probably good, and I think you can use BLAST from both, in addition to the phylogeny reconstruction.
Finding homologs and building phylogenetic trees, no trivial matter, good luck!
I think that is what I am going to have to do. Thanks for all the input!
Violeta's advice is spot on. Let me add to it that reconstructing phylogeny is no simple matter - while you can always get AN answer, building a phylogenetic tree without doing some background research on the methods first means your answer may not in fact be correct. Gather the closest relatives of your own sequence (as Violeta indicated). Include an "out group" - a more distantly related sequence - to act as the root. If possible try both a distance and a parsimony or Bayesian approach and compare their output.
Thanks everyone. I've started researching the various methods within Mega 6.0 so I think that is what I will use.
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