I have a set of sequences from 4 different species. I want to create clusters of sequences which are highly similar and show this information via a phylogenetic tree. I do not want to merge the sequences I just want to show them in the phylogenetic tree as a separate group
I suggest that you use "SDSC Biology Workbench": http://workbench.sdsc.edu/
I've been using this site for many years and it is an ideal "all-in-on" tool for protein and/or DNA sequence analysis as well as some structural modeling. It is very user friendly and the best tool of its kind on the web.
It has many sequence (protein and nucleic acid) analysis tool, including multisequence alignment and phylogenetic tree analysis.
regards,
Jeff
I would suggest MEGA as a good option: http://www.megasoftware.net/
Also, CLC Sequence viewer is quite intuitive and allows you to perform basic alignments and trees: http://www.clcbio.com/products/clc-sequence-viewer/
Both are freeware.
Trees generated by these programs are not so pretty, but you can export the dendrogram in Newick format and use other tools for visualization. I particularly like iTOL: http://itol.embl.de/
Dear Mehra,
in this regard MEGA is best one which embed all the tools for cluster analysis, Blast, sequence editing and phylogenetic analysis.Be happy
If you are looking for online tools to get it done (for small sequences) then visit http://www.phylogeny.fr/version2_cgi/index.cgi page.
I used "R package" . the best thing about R is free available, easy to handle large dataset and nice phylogenetic analysis using different clustering methods. only drawback is you should know the programming. if you are really interested to do then i will send you that book.
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