diff --git a/downloads-generation/models_class1_pan/GENERATE.WITH_HPC_CLUSTER.sh b/downloads-generation/models_class1_pan_select_only/GENERATE.WITH_HPC_CLUSTER.sh
similarity index 100%
rename from downloads-generation/models_class1_pan/GENERATE.WITH_HPC_CLUSTER.sh
rename to downloads-generation/models_class1_pan_select_only/GENERATE.WITH_HPC_CLUSTER.sh
diff --git a/downloads-generation/models_class1_pan/GENERATE.sh b/downloads-generation/models_class1_pan_select_only/GENERATE.sh
similarity index 100%
rename from downloads-generation/models_class1_pan/GENERATE.sh
rename to downloads-generation/models_class1_pan_select_only/GENERATE.sh
diff --git a/downloads-generation/models_class1_pan/additional_alleles.txt b/downloads-generation/models_class1_pan_select_only/additional_alleles.txt
similarity index 100%
rename from downloads-generation/models_class1_pan/additional_alleles.txt
rename to downloads-generation/models_class1_pan_select_only/additional_alleles.txt
diff --git a/downloads-generation/models_class1_pan/cluster_submit_script_header.mssm_hpc.lsf b/downloads-generation/models_class1_pan_select_only/cluster_submit_script_header.mssm_hpc.lsf
similarity index 100%
rename from downloads-generation/models_class1_pan/cluster_submit_script_header.mssm_hpc.lsf
rename to downloads-generation/models_class1_pan_select_only/cluster_submit_script_header.mssm_hpc.lsf
diff --git a/downloads-generation/models_class1_pan_unselected/GENERATE.WITH_HPC_CLUSTER.sh b/downloads-generation/models_class1_pan_unselected/GENERATE.WITH_HPC_CLUSTER.sh
index 4706e28316bb6f279d7cc2dd0d23e36f929f776e..53125eb7bec329ecbbd0d230b8afe809c1064204 100755
--- a/downloads-generation/models_class1_pan_unselected/GENERATE.WITH_HPC_CLUSTER.sh
+++ b/downloads-generation/models_class1_pan_unselected/GENERATE.WITH_HPC_CLUSTER.sh
@@ -1,94 +1 @@
-#!/bin/bash
-#
-# Train pan-allele MHCflurry Class I models. Supports re-starting a failed run.
-#
-# Uses an HPC cluster (Mount Sinai chimera cluster, which uses lsf job
-# scheduler). This would need to be modified for other sites.
-#
-set -e
-set -x
-
-DOWNLOAD_NAME=models_class1_pan_unselected
-SCRATCH_DIR=${TMPDIR-/tmp}/mhcflurry-downloads-generation
-SCRIPT_ABSOLUTE_PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/$(basename "${BASH_SOURCE[0]}")"
-SCRIPT_DIR=$(dirname "$SCRIPT_ABSOLUTE_PATH")
-
-mkdir -p "$SCRATCH_DIR"
-if [ "$1" != "continue-incomplete" ]
-then
-    echo "Fresh run"
-    rm -rf "$SCRATCH_DIR/$DOWNLOAD_NAME"
-    mkdir "$SCRATCH_DIR/$DOWNLOAD_NAME"
-else
-    echo "Continuing incomplete run"
-fi
-
-# Send stdout and stderr to a logfile included with the archive.
-LOG="$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.$(date +%s).txt"
-exec >  >(tee -ia "$LOG")
-exec 2> >(tee -ia "$LOG" >&2)
-
-# Log some environment info
-echo "Invocation: $0 $@"
-date
-pip freeze
-git status
-
-mhcflurry-downloads fetch data_curated allele_sequences random_peptide_predictions
-
-cd $SCRATCH_DIR/$DOWNLOAD_NAME
-
-export OMP_NUM_THREADS=1
-export PYTHONUNBUFFERED=1
-
-if [ "$1" != "continue-incomplete" ]
-then
-    cp $SCRIPT_DIR/generate_hyperparameters.py .
-    python generate_hyperparameters.py > hyperparameters.yaml
-fi
-
-for kind in combined
-do
-    EXTRA_TRAIN_ARGS=""
-    if [ "$1" == "continue-incomplete" ] && [ -d "models.${kind}" ]
-    then
-        echo "Will continue existing run: $kind"
-        EXTRA_TRAIN_ARGS="--continue-incomplete"
-    fi
-
-    mhcflurry-class1-train-pan-allele-models \
-        --data "$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2" \
-        --allele-sequences "$(mhcflurry-downloads path allele_sequences)/allele_sequences.csv" \
-        --pretrain-data "$(mhcflurry-downloads path random_peptide_predictions)/predictions.csv.bz2" \
-        --held-out-measurements-per-allele-fraction-and-max 0.25 100 \
-        --num-folds 4 \
-        --hyperparameters hyperparameters.yaml \
-        --out-models-dir $(pwd)/models.${kind} \
-        --worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
-        --verbosity 0 \
-        --cluster-parallelism \
-        --cluster-submit-command bsub \
-        --cluster-results-workdir ~/mhcflurry-scratch \
-        --cluster-script-prefix-path $SCRIPT_DIR/cluster_submit_script_header.mssm_hpc.lsf \
-        $EXTRA_TRAIN_ARGS
-done
-
-cp $SCRIPT_ABSOLUTE_PATH .
-bzip2 -f "$LOG"
-for i in $(ls LOG-worker.*.txt) ; do bzip2 -f $i ; done
-RESULT="$SCRATCH_DIR/${DOWNLOAD_NAME}.$(date +%Y%m%d).tar.bz2"
-tar -cjf "$RESULT" *
-echo "Created archive: $RESULT"
-
-# Split into <2GB chunks for GitHub
-PARTS="${RESULT}.part."
-# Check for pre-existing part files and rename them.
-for i in $(ls "${PARTS}"* )
-do
-    DEST="${i}.OLD.$(date +%s)"
-    echo "WARNING: already exists: $i . Moving to $DEST"
-    mv $i $DEST
-done
-split -b 2000M "$RESULT" "$PARTS"
-echo "Split into parts:"
-ls -lh "${PARTS}"*
+bash GENERATE.sh cluster
diff --git a/downloads-generation/models_class1_pan_unselected/GENERATE.sh b/downloads-generation/models_class1_pan_unselected/GENERATE.sh
index b6f2efae4e5cb259ff36ff6db02ced02e5c7e5a9..a161aa0e0497290f246b0422a6c763db9377626a 100755
--- a/downloads-generation/models_class1_pan_unselected/GENERATE.sh
+++ b/downloads-generation/models_class1_pan_unselected/GENERATE.sh
@@ -2,6 +2,11 @@
 #
 # Train pan-allele MHCflurry Class I models. Supports re-starting a failed run.
 #
+# Usage: GENERATE.sh <local|cluster> <fresh|continue-incomplete>
+#
+# cluster mode uses an HPC cluster (Mount Sinai chimera cluster, which uses lsf job
+# scheduler). This would need to be modified for other sites.
+#
 set -e
 set -x
 
@@ -10,8 +15,27 @@ SCRATCH_DIR=${TMPDIR-/tmp}/mhcflurry-downloads-generation
 SCRIPT_ABSOLUTE_PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/$(basename "${BASH_SOURCE[0]}")"
 SCRIPT_DIR=$(dirname "$SCRIPT_ABSOLUTE_PATH")
 
+if [ "$1" != "cluster" ]
+then
+    GPUS=$(nvidia-smi -L 2> /dev/null | wc -l) || GPUS=0
+    echo "Detected GPUS: $GPUS"
+
+    PROCESSORS=$(getconf _NPROCESSORS_ONLN)
+    echo "Detected processors: $PROCESSORS"
+
+    if [ "$GPUS" -eq "0" ]; then
+       NUM_JOBS=${NUM_JOBS-1}
+    else
+        NUM_JOBS=${NUM_JOBS-$GPUS}
+    fi
+    echo "Num jobs: $NUM_JOBS"
+    PARALLELISM_ARGS+=" --num-jobs $NUM_JOBS --max-tasks-per-worker 1 --gpus $GPUS --max-workers-per-gpu 1"
+else
+    PARALLELISM_ARGS+=" --cluster-parallelism --cluster-max-retries 3 --cluster-submit-command bsub --cluster-results-workdir $HOME/mhcflurry-scratch --cluster-script-prefix-path $SCRIPT_DIR/cluster_submit_script_header.mssm_hpc.gpu.lsf"
+fi
+
 mkdir -p "$SCRATCH_DIR"
-if [ "$1" != "continue-incomplete" ]
+if [ "$2" != "continue-incomplete" ]
 then
     echo "Fresh run"
     rm -rf "$SCRATCH_DIR/$DOWNLOAD_NAME"
@@ -31,29 +55,14 @@ date
 pip freeze
 git status
 
-mhcflurry-downloads fetch data_curated allele_sequences random_peptide_predictions
-
 cd $SCRATCH_DIR/$DOWNLOAD_NAME
 
-cp $SCRIPT_DIR/generate_hyperparameters.py .
-python generate_hyperparameters.py > hyperparameters.yaml
-
-GPUS=$(nvidia-smi -L 2> /dev/null | wc -l) || GPUS=0
-echo "Detected GPUS: $GPUS"
-
-PROCESSORS=$(getconf _NPROCESSORS_ONLN)
-echo "Detected processors: $PROCESSORS"
-
-if [ "$GPUS" -eq "0" ]; then
-   NUM_JOBS=${NUM_JOBS-1}
-else
-    NUM_JOBS=${NUM_JOBS-$GPUS}
-fi
-echo "Num jobs: $NUM_JOBS"
-
+export OMP_NUM_THREADS=1
 export PYTHONUNBUFFERED=1
 
-if [ "$1" != "continue-incomplete" ]
+cp $SCRIPT_DIR/additional_alleles.txt .
+
+if [ "$2" != "continue-incomplete" ]
 then
     cp $SCRIPT_DIR/generate_hyperparameters.py .
     python generate_hyperparameters.py > hyperparameters.yaml
@@ -61,25 +70,60 @@ fi
 
 for kind in combined
 do
-    EXTRA_TRAIN_ARGS=""
-    if [ "$1" == "continue-incomplete" ] && [ -d "models.${kind}" ]
+    CONTINUE_INCOMPLETE_ARGS=""
+    if [ "$2" == "continue-incomplete" ] && [ -d "models.unselected.${kind}" ]
     then
         echo "Will continue existing run: $kind"
-        EXTRA_TRAIN_ARGS="--continue-incomplete"
+        CONTINUE_INCOMPLETE_ARGS="--continue-incomplete"
     fi
 
+    ALLELE_SEQUENCES="$(mhcflurry-downloads path allele_sequences)/allele_sequences.csv"
+    TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2"
+
     mhcflurry-class1-train-pan-allele-models \
-        --data "$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2" \
-        --allele-sequences "$(mhcflurry-downloads path allele_sequences)/allele_sequences.csv" \
+        --data "$TRAINING_DATA" \
+        --allele-sequences "$ALLELE_SEQUENCES" \
         --pretrain-data "$(mhcflurry-downloads path random_peptide_predictions)/predictions.csv.bz2" \
         --held-out-measurements-per-allele-fraction-and-max 0.25 100 \
         --num-folds 4 \
-        --hyperparameters hyperparameters.yaml \
-        --out-models-dir models.${kind} \
+        --hyperparameters "$HYPERPARAMETERS" \
+        --out-models-dir $(pwd)/models.unselected.${kind} \
         --worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
-        --verbosity 0 \
-        --num-jobs $NUM_JOBS --max-tasks-per-worker 1 --gpus $GPUS --max-workers-per-gpu 1 \
-        $EXTRA_TRAIN_ARGS
+        $PARALLELISM_ARGS $CONTINUE_INCOMPLETE_ARGS
+done
+
+echo "Done training. Beginning model selection."
+
+for kind in combined
+do
+    MODELS_DIR="models.unselected.${kind}"
+
+    # For now we calibrate percentile ranks only for alleles for which there
+    # is training data. Calibrating all alleles would be too slow.
+    # This could be improved though.
+    ALLELE_LIST=$(bzcat "$MODELS_DIR/train_data.csv.bz2" | cut -f 1 -d , | grep -v allele | uniq | sort | uniq)
+    ALLELE_LIST+=$(echo " " $(cat additional_alleles.txt | grep -v '#') )
+
+    mhcflurry-class1-select-pan-allele-models \
+        --data "$MODELS_DIR/train_data.csv.bz2" \
+        --models-dir "$MODELS_DIR" \
+        --out-models-dir models.${kind} \
+        --min-models 2 \
+        --max-models 8 \
+        $PARALLELISM_ARGS
+    cp "$MODELS_DIR/train_data.csv.bz2" "models.${kind}/train_data.csv.bz2"
+
+    # For now we calibrate percentile ranks only for alleles for which there
+    # is training data. Calibrating all alleles would be too slow.
+    # This could be improved though.
+    time mhcflurry-calibrate-percentile-ranks \
+        --models-dir models.${kind} \
+        --match-amino-acid-distribution-data "$MODELS_DIR/train_data.csv.bz2" \
+        --motif-summary \
+        --num-peptides-per-length 100000 \
+        --allele $ALLELE_LIST \
+        --verbosity 1 \
+        $PARALLELISM_ARGS
 done
 
 cp $SCRIPT_ABSOLUTE_PATH .
@@ -102,3 +146,11 @@ split -b 2000M "$RESULT" "$PARTS"
 echo "Split into parts:"
 ls -lh "${PARTS}"*
 
+# Write out just the selected models
+# Move unselected into a hidden dir so it is excluded in the glob (*).
+mkdir .ignored
+mv models.unselected.* .ignored/
+RESULT="$SCRATCH_DIR/${DOWNLOAD_NAME}.selected.$(date +%Y%m%d).tar.bz2"
+tar -cjf "$RESULT" *
+mv .ignored/* . && rmdir .ignored
+echo "Created archive: $RESULT"
diff --git a/downloads-generation/models_class1_pan_unselected/additional_alleles.txt b/downloads-generation/models_class1_pan_unselected/additional_alleles.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37546e9e67154a141494f743ec5278900ca973cd
--- /dev/null
+++ b/downloads-generation/models_class1_pan_unselected/additional_alleles.txt
@@ -0,0 +1,3 @@
+# Additional alleles besides those in the training data to include in percentile rank calibration
+HLA-C*02:10
+HLA-A*02:20
\ No newline at end of file