Hello,
I am trying to find a bioinformatic tool to use on multiple sequences and get a devision into categories , until now I have used T-COFFEE score to devide to catagories., for example, a group with a low score compared to a group with a high score in T-COFFEE to emphesize the difference between the sequences or the same genome sequence in different organisms.
I have also used Excel to do all the statistics on the sequences like calculate all the BLAST results and devide to groups from that data as well.
Can anyone please reccomend a relible tool for that purpose? Hopefully one that I can submit all the DATA to and will get a devision into groups from the sequences, as well as a calculation of the differences between them?
Thank you in advance,
Oshrat Noked.
Hey,
I really do not know whether I got your idea right or not, but did you try clustalO or clustalW ? https://www.ebi.ac.uk/Tools/msa/clustalo/
Using this you will get a phylogenetic tree, on which you can cluster it, going as deep as you want to like 2 groups or n groups.
Hope this helps a bit.
Regards,
André
Hi, Oshrat Noked I think that CD-HIT is the bioinformatic tool you need. It is used to classify sequences based on its similitude (you can stablish similitude threshold), easy to use, fast and very accurate. Another way is to perform a phylogenetic tree based on multiple sequence alignment (MSA).
Best,
You can do clustering as well, many tools are available for k-means clustering and many other types of clustering as well.
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