# ama-qvalues

**Usage:** `ama-qvalues [options]`

**Description:**

Read an AMA output file and output each sequence name, p-value and q-value. At the end of file, the value of pi_0 (number of sequences not showing significant binding to motif) is shown, unless there are fewer than 100 p-values in the input.

**Input:**

Reads `standard input`

expecting an AMA output file.

**Options:**

- -seed <seed>
- seed for random numbers; default: 1
- -bootstraps <boot>
- number of bootstraps to perform while computing pi_0; default: 1000

**Output:**

For each sequence in the input, outputs the sequence name, the p-value of the sequence and the q-value (minimum false discovery rate).

If there are more than 99 sequences with p-values in the input then it provides an estimate of the number of sequences that contain the motif, otherwise known as the pi_0.

**See also:**