i have sequences of 16S r DNA. I used then for BLAST.
please guide me how to properly use this sequence for publishable analysis. I used Phylip for Tree generation but do not know its full use.
for one strain i sequenced it from two sides of a gene to get some overlap and then join it to know full sequence but do not know which software will help me.
so need help..
thanks.
Take out the sequences which are homologous to your sequences by blast and also put your gene sequences. Run phylip, view it in tree view and observe where are they falling close to.
Hi Arvind..
From your query it appears you are interested in molecular phylogenetic analysis of your sequences and other closely related organisms...As suggested by Preeti above ....get the sequences closest to you seqeunce or of the organisms in which you are interested...Do a good multiple sequence alignment first and then infer phyogeny..using any of the established and well quoted software, many of which are freely available from the authors....Phylip is good and commonly used..but it is 'command line' interfac based and all the modules of the progarm are not integrated...you have to run them one by one....If you still want to use it....'get the printout of the Manual, go through it and then do the analysis'...Doing it with knowing the parameters and capabilities of the programs you may make mistakes and data some times maye be difficult to interpret...
Other good interfaced program is MEGA (now 4-version is running)...which I also have used in my papers ...is really good, well integrated GUI babsed progarms and is also very well quoted in publications..
thanks Ajay
I have used Phylip and I am not happy with it coz there are many problems with it. I tried MEGA but did not know how to use it, so now I will try it.
actually i was trying for distance on tree to make it publishable, which is not easy with phylip.
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