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What are the blast and MCL options used to determine the EnsemblCompara MCL Families?

April 26, 2017blast determine Families MCL Options Used

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What are the blast and MCL options used to determine the EnsemblCompara MCL Families?

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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.