diff --git a/docs/commandline_tools.rst b/docs/commandline_tools.rst
index 20f7cbe56b36bcbbffc5037bb303ad7ce3ebb3ea..dc92a15c3c0bf39b9df44dde94dda9577dc0e2c5 100644
--- a/docs/commandline_tools.rst
+++ b/docs/commandline_tools.rst
@@ -18,4 +18,38 @@ See also the :ref:`tutorial <commandline_tutorial>`.
 .. autoprogram:: mhcflurry.downloads_command:parser
     :prog: mhcflurry-downloads
 
+.. _mhcflurry-class1-train-allele-specific-models:
+
+.. autoprogram:: mhcflurry.train_allele_specific_models_command:parser
+    :prog: mhcflurry-class1-train-allele-specific-models
+
+.. _mhcflurry-class1-select-allele-specific-models:
+
+.. autoprogram:: mhcflurry.select_allele_specific_models_command:parser
+    :prog: mhcflurry-class1-select-allele-specific-models
+
+.. _mhcflurry-class1-train-pan-allele-models:
+
+.. autoprogram:: mhcflurry.train_pan_allele_models_command:parser
+    :prog: mhcflurry-class1-train-pan-allele-models
+
+.. _mhcflurry-class1-select-pan-allele-models:
+
+.. autoprogram:: mhcflurry.select_pan_allele_models_command:parser
+    :prog: mhcflurry-class1-select-pan-allele-models
+
+.. _mhcflurry-class1-train-processing-models:
+
+.. autoprogram:: mhcflurry.train_processing_models_command:parser
+    :prog: mhcflurry-class1-train-processing-models
+
+.. _mhcflurry-class1-select-processing-models:
+
+.. autoprogram:: mhcflurry.select_processing_models_command:parser
+    :prog: mhcflurry-class1-select-processing-models
+
+.. _mhcflurry-class1-train-presentation-models:
+
+.. autoprogram:: mhcflurry.train_presentation_models_command:parser
+    :prog: mhcflurry-class1-train-presentation-models
 
diff --git a/docs/commandline_tutorial.rst b/docs/commandline_tutorial.rst
index 2014ec5538b4f8800ead01bb59ca8f105233e661..874f68606fb29f138e966345c3f07105cd1ca991 100644
--- a/docs/commandline_tutorial.rst
+++ b/docs/commandline_tutorial.rst
@@ -33,7 +33,7 @@ as well as an antigen processing (AP) predictor.
 .. note::
 
     The code we use for *generating* the downloads is in the
-    ``downloads_generation`` directory in the repository.
+    ``downloads_generation`` directory in the repository (https://github.com/openvax/mhcflurry/tree/master/downloads-generation)
 
 
 Generating predictions
@@ -99,7 +99,7 @@ sequences:
 .. literalinclude:: /example.fasta
 
 Here's the ``mhcflurry-predict-scan`` invocation to scan the proteins for
-binders to either of two MHC I genotypes:
+binders to either of two MHC I genotypes (using a 100 nM threshold):
 
 .. command-output::
     mhcflurry-predict-scan
@@ -107,8 +107,8 @@ binders to either of two MHC I genotypes:
         --alleles
             HLA-A*02:01,HLA-A*03:01,HLA-B*57:01,HLA-B*45:01,HLA-C*02:02,HLA-C*07:02
             HLA-A*01:01,HLA-A*02:06,HLA-B*44:02,HLA-B*07:02,HLA-C*01:02,HLA-C*03:01
-        --results-filtered affinity_percentile
-        --threshold-affinity-percentile 1.0
+        --results-filtered affinity
+        --threshold-affinity 100
     :nostderr:
 
 See the :ref:`mhcflurry-predict-scan` docs for more options.
diff --git a/docs/example.fasta b/docs/example.fasta
index ea095115509e108927979079136d5ff5b358d864..aa8623454fdc8aff287b66500a4e233c6f044493 100644
--- a/docs/example.fasta
+++ b/docs/example.fasta
@@ -1,6 +1,4 @@
 >protein1
-MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQV
-EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHH
+MSSSSTPVCPNGPGNCQV
 >protein2
-VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGA
-ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC
+MVENKRLLEGMEMIFGQVIPGA
diff --git a/docs/intro.rst b/docs/intro.rst
index 5b5f3581e5ab2dbd80193dcdd75f7f2bff0a8fb4..e1ebba0ccbde730090d37b729b30113da39b7147 100644
--- a/docs/intro.rst
+++ b/docs/intro.rst
@@ -2,7 +2,7 @@ Introduction and setup
 =======================
 
 MHCflurry is an open source package for peptide/MHC I binding affinity prediction. It
-attempts to provide competitive accuracy with a fast and documented implementation.
+aims to provide competitive accuracy with a fast and documented implementation.
 
 You can download pre-trained MHCflurry models fit to mass spec-identified MHC I
 ligands and peptide/MHC affinity measurements deposited in IEDB (plus a few other
@@ -63,7 +63,7 @@ tensorflow.
 
 .. code-block:: shell
 
-    $ conda create -q -n mhcflurry-env python=3.6 tensorflow
+    $ conda create -q -n mhcflurry-env python=3.6 'tensorflow<2.0.0'
     $ source activate mhcflurry-env
 
 Then continue as above: