CCPBioSim · harryswift01 · Sep 28, 2026 · Sep 28, 2026
diff --git a/example/all.eps → docs/source/_static/examples/all.eps b/example/all.eps → docs/source/_static/examples/all.eps
diff --git a/example/one_line.pbr322.toy.fa → ...e/_static/examples/one_line.pbr322.toy.fa b/example/one_line.pbr322.toy.fa → ...e/_static/examples/one_line.pbr322.toy.fa
diff --git a/....toy.fa.2.10.10.80.10.20.10000.100.1.html → ....toy.fa.2.10.10.80.10.20.10000.100.1.html b/....toy.fa.2.10.10.80.10.20.10000.100.1.html → ....toy.fa.2.10.10.80.10.20.10000.100.1.html
diff --git a/....fa.2.10.10.80.10.20.10000.100.1.txt.html → ....fa.2.10.10.80.10.20.10000.100.1.txt.html b/....fa.2.10.10.80.10.20.10000.100.1.txt.html → ....fa.2.10.10.80.10.20.10000.100.1.txt.html
diff --git a/example/pbr322.toy.compete.txt → ...e/_static/examples/pbr322.toy.compete.txt b/example/pbr322.toy.compete.txt → ...e/_static/examples/pbr322.toy.compete.txt
diff --git a/example/pbr322.toy.fa → docs/source/_static/examples/pbr322.toy.fa b/example/pbr322.toy.fa → docs/source/_static/examples/pbr322.toy.fa
diff --git a/docs/source/examples.rst b/docs/source/examples.rst
@@ -0,0 +1,39 @@
+Examples
+========
+
+Competition calculation
+------------------------
+
+Example of the output generated when the competition algorithm analyses the
+``pbr322.toy.fa`` sequence. These results are described in the Bioinformatics
+citation (see :doc:`citation`).
+
+Input file
+~~~~~~~~~~
+
+:download:`pbr322.toy.fa <_static/examples/pbr322.toy.fa>`
+
+Command
+~~~~~~~
+
+.. code-block:: bash
+
+   sist -f pbr322.toy.fa -a A -o pbr322.toy.compete.txt -b -p -r
+
+Output files
+~~~~~~~~~~~~
+
+* :download:`one_line.pbr322.toy.fa <_static/examples/one_line.pbr322.toy.fa>`,
+  the sequence file format required by Inverted Repeat Finder (IRF)
+* :download:`one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.html <_static/examples/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.html>`,
+  an IRF output file
+* :download:`one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.txt.html <_static/examples/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.txt.html>`,
+  an IRF output file
+* :download:`pbr322.toy.compete.txt <_static/examples/pbr322.toy.compete.txt>`,
+  the SIST output file
+
+Figure
+~~~~~~
+
+:download:`all.eps <_static/examples/all.eps>` represents graphically the
+output shown in ``pbr322.toy.compete.txt``.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -43,5 +43,6 @@ Run a competition calculation and write the result to a file:
    user-guide
    installation
    source-usage
+   examples
    development
    citation
diff --git a/docs/source/source-usage.rst b/docs/source/source-usage.rst
@@ -154,20 +154,5 @@ in the current working directory when these calculations are run.
 Example calculation
 -------------------
 
-The repository contains an example competition calculation based on
-``pbr322.toy.fa``.
-
-The command is:
-
-.. code-block:: bash
-
-   sist \
-       -f pbr322.toy.fa \
-       -a A \
-       -o pbr322.toy.compete.txt \
-       -b \
-       -p \
-       -r
-
-The example directory also contains IRF intermediate output and an EPS
-representation of the competition result.
+See :doc:`examples` for a full worked competition calculation, including
+downloadable input/output files and an EPS representation of the result.
diff --git a/example/README.txt b/example/README.txt