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What are the BLAST and MCL options used to determine the Ensembl Compara MCL Families?

The families are calculated with the following parameters.

 

For version v50 (and future versions), the blastall options are:

blastall -d $fastadb -i $qy_file -p blastp -e 0.00001 -v 250 -b 0

For the MCL clustering, the parameters are:

-I 2.1 -tf 'gq(50)' -scheme 6

For version v48 and previous versions, the parameters were:

-I 2.1 -P 10000 -S 1000 -R 1260 -pct 90


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