Hi! I'm using HHFilter 3.3.0 to sample sequences from MSA file which contains tens of thousands of homologous sequences .
The command is:
/userhome/anaconda3/envs/proteins/bin/hhfilter -i /userhome/data/TS2/msa/7KVT_B.a2m -o /userhome/data/TS2/7KVT_B_filter.a2m -id 90 -diff 512 -cov 0 -qid 0 -qsc -20.0
I set -diff 512 parameter, which should return 512 or more sequences that maximize diversity (the result is usually close to 512 ) according to the Help manual, but infact I got less than 512 sequences.
I set different numbers for the -diff parameter, and got diffrent results. The results are shown in the following figure, I think may be the number of sequences returned is weird. Is that normal?
Hi! I'm using HHFilter 3.3.0 to sample sequences from MSA file which contains tens of thousands of homologous sequences .
The command is:
/userhome/anaconda3/envs/proteins/bin/hhfilter -i /userhome/data/TS2/msa/7KVT_B.a2m -o /userhome/data/TS2/7KVT_B_filter.a2m -id 90 -diff 512 -cov 0 -qid 0 -qsc -20.0I set
-diff 512parameter, which should return 512 or more sequences that maximize diversity (the result is usually close to 512 ) according to the Help manual, but infact I got less than 512 sequences.I set different numbers for the
-diffparameter, and got diffrent results. The results are shown in the following figure, I think may be the number of sequences returned is weird. Is that normal?