I use different online tools like LAST, BLAST, VISTA etc, and want results in figures but all these tools give error regarding the size of data. like size of data is greater or somewhat else. kindly help me in this to complete my work.
Did you tried MAFFT or MUSCLE?
try it, may be helpful.
http://www.ebi.ac.uk/Tools/msa/mafft/
http://www.ebi.ac.uk/Tools/msa/muscle/
JSpecies is the best way to do that. It is a nice java-based tool that gives you nice metrics about whole genome comparison based on BLAST, Mummer algorithms, and Kmers.
Hi Muhammed,
you might also have a look at Mauve:
http://darlinglab.org/mauve/mauve.html
It's pretty quick and easy generally for chromosome or small genome-sized (i.e., bacterial) comparisons.
Hi Muhammad,
have you tried dot plot?
gepard (http://bioinformatics.oxfordjournals.org/content/23/8/1026.full) is a user-friendly, java-based application for quick creation of dot plots. It also works with large sequences.
good luck
Massimo
Hey Muhammad,
I agree with Massimo; a dot plot would be the way to go. Have you checked out CoGe? Your species may be on there and there are some really neat tools for comparative genomics.
https://genomevolution.org/coge/
Adam
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