diff --git a/README.md b/README.md index fdfd2c8bb5c520a42764881cf135621be1eb0006..4f1d5a1ccccae96bd3cfe5794be64c4ce0ce51ff 100644 --- a/README.md +++ b/README.md @@ -7,11 +7,12 @@ wGRR is a set of scripts to calculate the weighted Gene Repertoire Relatedness ( wGRR(A,B) = \frac{\sum_{i}{id(A_i,B_i)}}{min(P_A,P_B)} ``` where -* $`id(A_i,B_i)`$ is the identity score for each BBH pair between element $`A`$ and element $`B`$ -* $`min(P_A,P_B)`$ is the number of proteins in the smallest of $`A`$ and $`B`$ elements. +* $`i`$ is the number of BBH between elements $`A`$ and $`B`$ +* $`id(A_i,B_i)`$ is the identity score of BBH $`i`$ +* $`P_A`$ and $`P_B`$ are the numbers of proteins of $`A`$ and $`B`$ respectively **NOTE** -`wGRR` calculates 3 versions of the wGRR depending on which BBH pairs are considered (numerator) and what proteins should be counted (denominator). See the `Output` section of this manual for more explanations. +`wGRR` calculates 3 versions of the wGRR score depending on which BBH are considered (numerator) and what proteins should be counted (denominator). See the `Output` section of this manual for more explanations. ### Dependencies BBH are defined by all versus all protein comparisons using [MMseqs2][1]. @@ -105,6 +106,6 @@ wGRR3 also uses the protein families. But this time, if two BBH pairs are found Common3 is the number of protein families containing at least one BBH divided by the mean nProt3 of two elements. - + [1]: https://mmseqs.com/