NEFF 1.0

written by

Bernhard Haubold and Thomas Wiehe

NEFF computes the SNP-effective sample size of a "ragged" alignment.

The raw data for SNP-surveys often consists of a subject sequence with some regions covered by one or more fragments. Given such a "ragged" alignment", we ask, how many times the full subject sequence would need to be resequenced in order to obtain the same capacity to detect SNPs as the actual data; this quantity is designated neff. NEFF takes as input the output of a BLAST search and returns neff.

Example data


Paste BLAST results:

theta (per nucleotide, optional):