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+#+title: percent nucleotide identity threshold (pnit?)
+
+* input
+csv file, first row and first column are names, every other item is
+the % identity of the names corresponding to the current cell.
+
+#+name: input-table-example
+|      | seq1 | seq2 | seq3 |
+| seq1 |      |      |      |
+| seq2 | 0.9  |      |      |
+| seq3 | 0.32 | 0.11 |      |
+
+this shows ~seq2~ is 90% identical to ~seq1~, and ~seq3~ is 32% and 11%
+identical to ~seq1~ and ~seq2~, respectively.
+
+the csv file would look like this:
+#+name: input-csv-example
+#+begin_src text
+  ,seq1,seq2,seq3
+  seq1,,,
+  seq2,0.9,,
+  seq3,0.32,0.11,
+#+end_src
+
+* output
+csv file, two column, representing a pair where the value is at least
+as large a given threshold.
+
+given [[input-table-example][the example input table]], at a threshold of 32%, we should get:
+#+name: output-table-example-32
+| seq2 | seq1 |
+| seq3 | seq1 |
+
+or, in csv:
+#+name: output-csv-example
+#+begin_src text
+  seq2,seq1
+  seq3,seq1
+#+end_src
+
+* runners
+#+name: process
+#+begin_src shell :results file :file n-401-94.csv :var threshold=94.0 filename="inputs/n-401.csv"
+  guix shell perl -- ./pairwise.pl $threshold $filename
+#+end_src
+
+#+RESULTS: process
+[[file:n-401-94.csv]]
+
+#+call: process[:file n-402-90.5.csv](threshold=90.5, filename="n-402.csv")
+
+#+RESULTS:
+[[file:n-402-90.5.csv]]
+
+#+call: process[:file n-402-93.5.csv](threshold=93.5, filename="n-402.csv")
+
+#+RESULTS:
+[[file:n-402-93.5.csv]]
+