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README.md

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 # mhctools
+
 Python interface to running command-line and web-based MHC binding predictors.
 
 ## Commandline examples
 
 ### Prediction for user-supplied peptide sequences
+
 ```sh
 mhctools --sequence SIINFEKL SIINFEKLQ --mhc-predictor netmhc --mhc-alleles A0201
 ```
 
 ### Automatically extract peptides as subsequences of specified length
+
 ```sh
 mhctools --sequence AAAQQQSIINFEKL --extract-subsequences --mhc-peptide-lengths 8-10 --mhc-predictor mhcflurry --mhc-alleles A0201
 ```
@@ -54,18 +58,20 @@ for binding_prediction in binding_predictions:
 ## API
 
 The following MHC binding predictors are available in `mhctools`:
-* `MHCflurry`: open source predictor installed by default with `mhctools`, requires the user run `mhcflurry-downloads fetch` first to download MHCflurry models
-* `NetMHC3`: requires locally installed version of [NetMHC 3.x](http://www.cbs.dtu.dk/services/NetMHC-3.4/)
-* `NetMHC4`: requires locally installed version of [NetMHC 4.x](http://www.cbs.dtu.dk/services/NetMHC/)
-* `NetMHC`: a wrapper function to automatically use `NetMHC3` or `NetMHC4` depending on what's installed.
-* `NetMHCpan`: requires locally installed version of [NetMHCpan](http://www.cbs.dtu.dk/services/NetMHCpan/)
-* `NetMHCIIpan`: requires locally installed version of [NetMHCIIpan](http://www.cbs.dtu.dk/services/NetMHCIIpan/)
-* `NetMHCcons`: requires locally installed version of [NetMHCcons](http://www.cbs.dtu.dk/services/NetMHCcons/)
-* `IedbMhcClass1`: Uses IEDB's REST API for class I binding predictions.
-* `IedbMhcClass2`: Uses IEDB's REST API for class II binding predictions.
-* `RandomBindingPredictor`: Creates binding predictions with random IC50 and percentile rank values.
+
+- `MHCflurry`: open source predictor installed by default with `mhctools`, requires the user run `mhcflurry-downloads fetch` first to download MHCflurry models
+- `NetMHC3`: requires locally installed version of [NetMHC 3.x](http://www.cbs.dtu.dk/services/NetMHC-3.4/)
+- `NetMHC4`: requires locally installed version of [NetMHC 4.x](http://www.cbs.dtu.dk/services/NetMHC/)
+- `NetMHC`: a wrapper function to automatically use `NetMHC3` or `NetMHC4` depending on what's installed.
+- `NetMHCpan`: requires locally installed version of [NetMHCpan](http://www.cbs.dtu.dk/services/NetMHCpan/)
+- `NetMHCIIpan`: requires locally installed version of [NetMHCIIpan](http://www.cbs.dtu.dk/services/NetMHCIIpan/)
+- `NetMHCcons`: requires locally installed version of [NetMHCcons](http://www.cbs.dtu.dk/services/NetMHCcons/)
+- `IedbMhcClass1`: Uses IEDB's REST API for class I binding predictions.
+- `IedbMhcClass2`: Uses IEDB's REST API for class II binding predictions.
+- `RandomBindingPredictor`: Creates binding predictions with random IC50 and percentile rank values.
 
 Every binding predictor is constructed with an `alleles` argument specifying the HLA type for which to make predictions. Predictions are generated by calling the `predict` method with a dictionary mapping sequence IDs or names to amino acid sequences.
 
-Additionally there is a module for running the [NetChop](http://www.cbs.dtu.dk/services/NetChop)  proteosomal cleavage predictor:
-* `NetChop`: requires locally installed version of [NetChop-3.1](http://www.cbs.dtu.dk/services/NetChop/)
+Additionally there is a module for running the [NetChop](http://www.cbs.dtu.dk/services/NetChop) proteosomal cleavage predictor:
+
+- `NetChop`: requires locally installed version of [NetChop-3.1](http://www.cbs.dtu.dk/services/NetChop/)