I am working with NCBI BLAST to compare few aa sequences with database records. I can choose, after analysis, the option "Distance tree of results". I know that we can choose results for each sequence separately but is there an option to draw a tree for all sequences (on one tree). I know that I can copy similar sequences from databases to MEGA (for example) and make an analysis using this software but it will be very "painful" and time-consuming to do. Is there any possibility to do it with NCBI tools or other on line scripts?
http://www.ebi.ac.uk/Tools/msa/clustalw2/
http://www.molbiol-tools.ca/Alignments.htm
http://www.expasy.org/tools/
http://people.virginia.edu/~wrp/cshl06/smith_res.html
http://www.geneinfinity.org/sp/sp_proteinalign.html
Good luck :)
thanks:)
but still I need a tool which could compare not only my sequences with each other but with results from databases at the same time. This is working in NCBI BLAST but it is comparing each sequence separately. I need one tree with my sequences and sequences from databases.
You need to screen through all the sequences and download the ones you want to compare (note that the same sequence may be repeated in the same or different database), then you create one file with all sequences in fasta format for example and you upload the file to one of the tools Mr Nowicki quoted above, ClustalW for example. This tool aligns all your sequences and can draw a tree of all.
i dont have the software Genius (http://www.geneious.com) with me now, but i remember when I was using it last year, there was something as you have mentioned. you can download the trial version. You can search, download, align and analyse your sequences in the same window using different options.
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