I have installed the blast standalone latest version 2.2.25 with the help of the installation guide http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/pc_setup.html. I ran the blast with a 14Mb fasta file by changing the parameters:
-S 1.5 -L 0.9. But I could not get the cluster properly and I got a cluster file containing only 3 clusters and an error.log empty text file after running. Even the no. of sequences are reading while running. But When I tried online submission of some of my sequences, I got few clusters. Kindly help out the problem to get the correct clusters Using BLASTCLUST. But other different blast of the package except this are not getting correct result. Kindly help me as soon as possible.
with best regards, K. Pawankumar