diff --git a/client/src/app/core/utils/counter.util.ts b/client/src/app/core/utils/counter.util.ts
new file mode 100644
index 00000000..7110bb08
--- /dev/null
+++ b/client/src/app/core/utils/counter.util.ts
@@ -0,0 +1,12 @@
+// keeps an internal count that is incremented at each get call
+class Counter {
+
+  private _count = 0;
+
+  getCount() {
+    return this._count++;
+  }
+}
+
+// singleton
+export const counter = new Counter();
diff --git a/client/src/app/core/utils/index.ts b/client/src/app/core/utils/index.ts
index aa9fdb99..ca80a4d3 100644
--- a/client/src/app/core/utils/index.ts
+++ b/client/src/app/core/utils/index.ts
@@ -1,5 +1,6 @@
 import { arrayFlatten } from './array-flatten.util';
 import { arrayIsEqual } from './array-is-equal.util';
+import { counter } from './counter.util';
 import { elementIsVisible } from './element-is-visible.util';
 import { memoizeArray } from './memoize-array.util';
 import { saveFile } from './save-file.util';
@@ -8,6 +9,7 @@ import { saveFile } from './save-file.util';
 export const utils: any[] = [
   arrayFlatten,
   arrayIsEqual,
+  counter,
   elementIsVisible,
   memoizeArray,
   saveFile,
@@ -16,6 +18,7 @@ export const utils: any[] = [
 
 export * from './array-flatten.util';
 export * from './array-is-equal.util';
+export * from './counter.util';
 export * from './element-is-visible.util';
 export * from './memoize-array.util';
 export * from './save-file.util';
diff --git a/client/src/app/gene/components/viewers/micro/micro.shim.ts b/client/src/app/gene/components/viewers/micro/micro.shim.ts
index ed246f0e..b50d1171 100644
--- a/client/src/app/gene/components/viewers/micro/micro.shim.ts
+++ b/client/src/app/gene/components/viewers/micro/micro.shim.ts
@@ -84,7 +84,7 @@ function _tracksToData(tracks, genes) {
 export function microShim(clusterID, queryTracks, tracks, genes) {
   // create data
   const filteredTracks = tracks.filter((t) => t.cluster == clusterID);
-  const data = _tracksToData(tracks, genes);
+  const data = _tracksToData(filteredTracks, genes);
   // identify bold tracks
   const bold = [];
   filteredTracks.forEach((t, i) => {
diff --git a/client/src/app/gene/gene-routing.module.ts b/client/src/app/gene/gene-routing.module.ts
index 81b21cab..9575a954 100644
--- a/client/src/app/gene/gene-routing.module.ts
+++ b/client/src/app/gene/gene-routing.module.ts
@@ -7,9 +7,13 @@ import { GeneComponent, HeaderLeftComponent, HeaderRightComponent }
 
 export const routes: Routes = [
   {
-    path: ':source/:gene',
+    path: '',
     component: GeneComponent,
   },
+  //{
+  //  path: ':source/:gene',
+  //  component: GeneComponent,
+  //},
   {
     path: '',
     component: HeaderLeftComponent,
diff --git a/client/src/app/gene/models/params/clustering.model.ts b/client/src/app/gene/models/params/clustering.model.ts
index ad7508f3..351d8376 100644
--- a/client/src/app/gene/models/params/clustering.model.ts
+++ b/client/src/app/gene/models/params/clustering.model.ts
@@ -11,7 +11,7 @@ export class ClusteringParams implements Params {
 
   constructor(
     public linkage: string = 'average',  // TODO: remove magic string
-    public threshold: number = 10) {
+    public threshold: number = 20) {
   }
 
   formControls(): any {
diff --git a/client/src/app/gene/models/shims/family-count-map.ts b/client/src/app/gene/models/shims/family-count-map.ts
new file mode 100644
index 00000000..26872018
--- /dev/null
+++ b/client/src/app/gene/models/shims/family-count-map.ts
@@ -0,0 +1,14 @@
+export type FamilyCountMap = {[key: string]: number};
+
+
+export function familyCountMap(families: string[]): FamilyCountMap {
+  const reducer = (accumulator, family) => {
+      if (!(family in accumulator)) {
+        accumulator[family] = 0;
+      }
+      accumulator[family] += 1;
+      return accumulator;
+    };
+  const map = families.reduce(reducer, {});
+  return map;
+}
diff --git a/client/src/app/gene/models/shims/index.ts b/client/src/app/gene/models/shims/index.ts
index f829a0e8..d1eb245a 100644
--- a/client/src/app/gene/models/shims/index.ts
+++ b/client/src/app/gene/models/shims/index.ts
@@ -1,5 +1,6 @@
 export * from './block-index-map';
 export * from './endpoint-genes';
+export * from './family-count-map';
 export * from './gene-map';
 export * from './macro-blocks';
 export * from './name-source-id';
diff --git a/client/src/app/gene/store/actions/chromosome.actions.ts b/client/src/app/gene/store/actions/chromosome.actions.ts
index d7cc7959..7cf9edc7 100644
--- a/client/src/app/gene/store/actions/chromosome.actions.ts
+++ b/client/src/app/gene/store/actions/chromosome.actions.ts
@@ -1,4 +1,5 @@
 import { Action } from '@ngrx/store';
+import { counter } from '@gcv/core/utils';
 import { Track } from '@gcv/gene/models';
 
 export const GET = '[CHROMOSOME] GET';
@@ -7,6 +8,7 @@ export const GET_FAILURE = '[CHROMOSOME] GET_FAILURE';
 
 export class Get implements Action {
   readonly type = GET;
+  readonly id = counter.getCount();
   constructor(public payload: {name: string, source: string}) { }
 }
 
diff --git a/client/src/app/gene/store/actions/gene.actions.ts b/client/src/app/gene/store/actions/gene.actions.ts
index bde885d9..4e582ffe 100644
--- a/client/src/app/gene/store/actions/gene.actions.ts
+++ b/client/src/app/gene/store/actions/gene.actions.ts
@@ -1,12 +1,15 @@
 import { Action } from '@ngrx/store';
+import { counter } from '@gcv/core/utils';
 import { Gene, Track } from '@gcv/gene/models';
 
 export const GET = '[GENE] GET';
 export const GET_SUCCESS = '[GENE] GET_SUCCESS';
 export const GET_FAILURE = '[GENE] GET_FAILURE';
 
+
 export class Get implements Action {
   readonly type = GET;
+  readonly id = counter.getCount();
   constructor(public payload: {names: string[], source: string}) { }
 }
 
diff --git a/client/src/app/gene/store/effects/chromosome.effects.ts b/client/src/app/gene/store/effects/chromosome.effects.ts
index bb2ef947..780363ab 100644
--- a/client/src/app/gene/store/effects/chromosome.effects.ts
+++ b/client/src/app/gene/store/effects/chromosome.effects.ts
@@ -3,11 +3,13 @@ import { Injectable } from '@angular/core';
 // store
 import { Effect, Actions, ofType } from '@ngrx/effects';
 import { of } from 'rxjs';
-import { catchError, filter, map, mergeMap, switchMap } from 'rxjs/operators';
+import { catchError, filter, map, mergeMap, switchMap, withLatestFrom }
+  from 'rxjs/operators';
 import { Store } from '@ngrx/store';
 import * as chromosomeActions from '@gcv/gene/store/actions/chromosome.actions';
 import * as fromRoot from '@gcv/gene/store/reducers';
 import * as fromChromosome from '@gcv/gene/store/selectors/chromosome/';
+import { TrackID, trackID } from '@gcv/gene/store/utils';
 // app
 import { ChromosomeService } from '@gcv/gene/services';
 
@@ -24,15 +26,28 @@ export class ChromosomeEffects {
   getSelected$ = this.store
   .select(fromChromosome.getUnloadedSelectedChromosomeIDs).pipe(
     filter((ids) => ids.length > 0),
-    switchMap((ids) =>  ids.map((id) => new chromosomeActions.Get(id))),
+    mergeMap((ids) => ids.map((id) => new chromosomeActions.Get(id))),
   );
 
   // get chromosome via the chromosome service
   @Effect()
   getChromosome$ = this.actions$.pipe(
     ofType(chromosomeActions.GET),
-    map((action: chromosomeActions.Get) => action.payload),
-    mergeMap(({name, source}) => {
+    map((action: chromosomeActions.Get) => {
+      return {action: action.id, ...action.payload};
+    }),
+    withLatestFrom(this.store.select(fromChromosome.getLoading)),
+    mergeMap(([{action, name, source}, loading]) => {
+      // get loaded/loading genes
+      const actionTrackID =
+        ({name, source, action}) => `${trackID(name, source)}:${action}`;
+      const loadingIDs = new Set(loading.map(actionTrackID));
+      // only load chromosome if action is loading
+      const id = actionTrackID({action, name, source});
+      const chromosomeID = trackID(name, source);
+      if (!loadingIDs.has(id)) {
+        return [];
+      }
       return this.chromosomeService.getChromosome(name, source).pipe(
         map((chromosome) => {
           return new chromosomeActions.GetSuccess({chromosome});
diff --git a/client/src/app/gene/store/effects/gene.effects.ts b/client/src/app/gene/store/effects/gene.effects.ts
index 54475feb..66bdc89e 100644
--- a/client/src/app/gene/store/effects/gene.effects.ts
+++ b/client/src/app/gene/store/effects/gene.effects.ts
@@ -29,34 +29,45 @@ export class GeneEffects {
   getSelected$ = this.store.select(fromGene.getUnloadedSelectedGeneIDs).pipe(
     filter((ids) => ids.length > 0),
     switchMap((ids) => {
-      const id2action = ({name, source}) => {
-          return new geneActions.Get({names: [name], source});
+      // bin ids by source
+      const reducer = (accumulator, {name, source}) => {
+          if (!(source in accumulator)) {
+            accumulator[source] = [];
+          }
+          accumulator[source].push(name);
+          return accumulator;
         };
-      const actions = ids.map(id2action);
+      const geneBins = ids.reduce(reducer, {});
+      // make a gene request action for each source bin
+      const actions = Object.entries(geneBins)
+        .map(([source, names]: [string, string[]]) => {
+          return new geneActions.Get({names, source});
+        });
       return actions;
     }),
   );
 
-  // TODO: when loading multi route, take loading and failed genes into
-  // consideration
-
   // get genes via the gene service
   @Effect()
   getGenes$ = this.actions$.pipe(
     ofType(geneActions.GET),
-    map((action: geneActions.Get) => action.payload),
-    withLatestFrom(this.store.select(fromGene.getGeneState)),
-    concatMap(([{names, source}, state]) => {
+    map((action: geneActions.Get) => ({action: action.id, ...action.payload})),
+    withLatestFrom(this.store.select(fromGene.getLoading)),
+    concatMap(([{action, names, source}, loading]) => {
       // get loaded/loading genes
-      const loadingIDs = new Set(state.loading.map(geneID));
-      const loadedIDs = new Set(state.loaded.map(geneID));
-      // filter out genes that are already loaded or loading
-      const filteredNamess = names.filter((n) => {
-          const gID = geneID(n, source);
-          return !loadingIDs.has(gID) && !loadedIDs.has(gID);
+      const actionGeneID =
+        ({name, source, action}) => `${geneID(name, source)}:${action}`;
+      const loadingIDs = new Set(loading.map(actionGeneID));
+      // only keep genes whose action is loaded
+      const filteredNames = names.filter((name) => {
+          const id = actionGeneID({name, source, action});
+          return loadingIDs.has(id);
         });
       // get the genes
-      return this.geneService.getGenes(names, source).pipe(
+      if (filteredNames.length == 0) {
+        return [];
+      }
+      return this.geneService.getGenes(filteredNames, source).pipe(
         map((genes: Gene[]) =>  new geneActions.GetSuccess({genes})),
         catchError((error) => of(new geneActions.GetFailure({names, source})))
       );
@@ -66,9 +77,7 @@ export class GeneEffects {
   // get all genes for the selected micro-tracks
   @Effect()
   getMicroTrackGenes$ = this.store.select(fromMicroTracks.getAllMicroTracks).pipe(
-    switchMap((tracks) => {
-      return geneActions.tracksToGetGeneActions(tracks);
-    }),
+    switchMap((tracks) => geneActions.tracksToGetGeneActions(tracks)),
   );
 
 }
diff --git a/client/src/app/gene/store/reducers/chromosome.reducer.ts b/client/src/app/gene/store/reducers/chromosome.reducer.ts
index 834bacc5..cf568985 100644
--- a/client/src/app/gene/store/reducers/chromosome.reducer.ts
+++ b/client/src/app/gene/store/reducers/chromosome.reducer.ts
@@ -1,17 +1,16 @@
 // A chromosome is an instance of Track that represents an entire chromosome
 // as an ordered list of genes and a corresponding list of gene families. This
-// file provides an NgRx reducer and selectors for storing and accessing
-// chromosome data. Specifically, a chromosome is loaded as a Track for each
-// gene provided by the user. These Tracks are stored by the chromosome reducer
-// and made available via selectors. This includes a selector that provides the
-// neighborhood each user provided gene occurs is as a slice of the gene's
-// chromosome.
+// file provides an NgRx reducer for storing chromosome data. Specifically, a
+// chromosome is loaded as a Track for each gene provided by the user. These
+// Tracks are stored by the chromosome reducer and made available via selectors.
+// This includes a selector that provides the neighborhood each user provided
+// gene occurs is as a slice of the gene's chromosome - a micro-track.
 
 // NgRx
 import { createEntityAdapter, EntityState } from '@ngrx/entity';
 // store
 import * as chromosomeActions from '@gcv/gene/store/actions/chromosome.actions';
-import { TrackID, trackID } from '@gcv/gene/store/utils';
+import { ActionID, TrackID, trackID } from '@gcv/gene/store/utils';
 // app
 import { Track } from '@gcv/gene/models';
 
@@ -23,17 +22,14 @@ const adapter = createEntityAdapter<Track>({
   selectId: (e) => trackID(e.name, e.source)
 });
 
-// TODO: is loaded even necessary or can it be derived from entity ids and
 // selectedChromosomeIDs selector?
 export interface State extends EntityState<Track> {
   failed: TrackID[];
-  loaded: TrackID[];
-  loading: TrackID[];
+  loading: (TrackID & ActionID)[];
 }
 
 const initialState: State = adapter.getInitialState({
   failed: [],
-  loaded: [],
   loading: [],
 });
 
@@ -43,9 +39,20 @@ export function reducer(
 ): State {
   switch (action.type) {
     case chromosomeActions.GET:
+      const loadingIDs = new Set(state.loading.map(trackID));
+      const id = trackID(action.payload);
+      const loading = [];
+      if (!loadingIDs.has(id) && !(id in state.entities)) {
+        loading.push({action: action.id, ...action.payload});
+      }
+      const failed = state.failed.filter(({name, source}) => {
+          const fID = trackID(name, source);
+          return fID === id;
+        });
       return {
         ...state,
-        loading: state.loading.concat([action.payload]),
+        loading: state.loading.concat(loading),
+        failed,
       };
     case chromosomeActions.GET_SUCCESS:
     {
@@ -55,7 +62,6 @@ export function reducer(
         chromosome,
         {
           ...state,
-          loaded: state.loaded.concat(id),
           loading: state.loading.filter(({name, source}) => {
             return !(name === id.name && source === id.source);
           }),
diff --git a/client/src/app/gene/store/reducers/gene.reducer.ts b/client/src/app/gene/store/reducers/gene.reducer.ts
index a3d89cca..7fdab43f 100644
--- a/client/src/app/gene/store/reducers/gene.reducer.ts
+++ b/client/src/app/gene/store/reducers/gene.reducer.ts
@@ -1,8 +1,8 @@
 // A Gene is a second class citizen in the GCV, that is, other than dictating
 // what chromosomes are loaded, all visualizations, algorithms, and auxiliary
 // models are derived from the gene families of the Track model. As such, genes
-// are loaded on an as needed basis. This file contains an NgRx reducer and
-// selectors for storing and accessing Genes.
+// are loaded on an as needed basis. This file contains an NgRx reducer for
+// storing Genes.
 
 // NgRx
 import { createEntityAdapter, EntityState } from '@ngrx/entity';
@@ -10,6 +10,7 @@ import { createEntityAdapter, EntityState } from '@ngrx/entity';
 import * as geneActions from '@gcv/gene/store/actions/gene.actions';
 // app
 import { Gene } from '@gcv/gene/models';
+import { ActionID } from '@gcv/gene/store/utils';
 
 declare var Object: any;  // because TypeScript doesn't support Object.values
 
@@ -32,17 +33,14 @@ const adapter = createEntityAdapter<Gene>({
   selectId: (e) => geneID(e.name, e.source)
 });
 
-// TODO: is loaded even necessary or can it be derived from entity ids and
 // selectedGeneIDs selector?
 export interface State extends EntityState<Gene> {
   failed: GeneID[];
-  loaded: GeneID[];
-  loading: GeneID[];
+  loading: (GeneID & ActionID)[];
 }
 
 const initialState: State = adapter.getInitialState({
   failed: [],
-  loaded: [],
   loading: [],
 });
 
@@ -53,10 +51,24 @@ export function reducer(
   switch (action.type) {
     case geneActions.GET:
       const source = action.payload.source;
-      const loading = action.payload.names.map((name) => ({name, source}));
+      const loadingIDs = new Set(state.loading.map(geneID));
+      const loading = action.payload.names
+        .filter((name) => {
+          const id = geneID(name, source);
+          return !loadingIDs.has(id) && !(id in state.entities);
+        })
+        .map((name) => {
+          return {name, source, action: action.id};
+        });
+      const newLoadingIDs = new Set(loading.map(geneID));
+      const failed = state.failed.filter(({name, source}) => {
+          const id = geneID(name, source);
+          return !newLoadingIDs.has(id);
+        });
       return {
         ...state,
         loading: state.loading.concat(loading),
+        failed,
       };
     case geneActions.GET_SUCCESS:
     {
@@ -72,7 +84,6 @@ export function reducer(
         genes,
         {
           ...state,
-          loaded: state.loaded.concat(loaded),
           loading,
         },
       );
diff --git a/client/src/app/gene/store/selectors/chromosome/chromosome-state.selector.ts b/client/src/app/gene/store/selectors/chromosome/chromosome-state.selector.ts
index a2165bd2..f1495a0c 100644
--- a/client/src/app/gene/store/selectors/chromosome/chromosome-state.selector.ts
+++ b/client/src/app/gene/store/selectors/chromosome/chromosome-state.selector.ts
@@ -10,3 +10,9 @@ export const getChromosomeState = createSelector(
   fromModule.getGeneModuleState,
   state => state[chromosomeFeatureKey]
 );
+
+
+export const getLoading = createSelector(
+  getChromosomeState,
+  state => state.loading,
+);
diff --git a/client/src/app/gene/store/selectors/chromosome/clustered-chromosomes.selector.ts b/client/src/app/gene/store/selectors/chromosome/clustered-chromosomes.selector.ts
index e8b02341..c651a065 100644
--- a/client/src/app/gene/store/selectors/chromosome/clustered-chromosomes.selector.ts
+++ b/client/src/app/gene/store/selectors/chromosome/clustered-chromosomes.selector.ts
@@ -10,7 +10,8 @@ import { Track } from '@gcv/gene/models';
 import { ClusterMixin } from '@gcv/gene/models/mixins';
 
 
-export const getSelectedChromosomesForCluster = (id: number) => createSelector(
+export const getSelectedChromosomesForCluster =
+(id: number) => createSelector(
   getSelectedChromosomes,
   getSelectedMicroTracksForCluster(id),
   (chromosomes: Track[], tracks: (Track | ClusterMixin)[]): Track[] => {
diff --git a/client/src/app/gene/store/selectors/chromosome/selected-chromosomes.selector.ts b/client/src/app/gene/store/selectors/chromosome/selected-chromosomes.selector.ts
index 8369a3ae..73a11367 100644
--- a/client/src/app/gene/store/selectors/chromosome/selected-chromosomes.selector.ts
+++ b/client/src/app/gene/store/selectors/chromosome/selected-chromosomes.selector.ts
@@ -83,7 +83,7 @@ export const getUnloadedSelectedChromosomeIDs = createSelector(
   getSelectedChromosomeIDs,
   (state: State, ids: TrackID[]): TrackID[] => {
     const loadingIDs = new Set(state.loading.map(trackID));
-    const loadedIDs = new Set(state.loaded.map(trackID));
+    const loadedIDs = new Set(state.ids as string[]);
     const unloadedIDs = ids.filter((id) => {
         const idString = trackID(id);
         return !loadingIDs.has(idString) && !loadedIDs.has(idString);
diff --git a/client/src/app/gene/store/selectors/gene/gene-state.selector.ts b/client/src/app/gene/store/selectors/gene/gene-state.selector.ts
index f9d29684..49b3d217 100644
--- a/client/src/app/gene/store/selectors/gene/gene-state.selector.ts
+++ b/client/src/app/gene/store/selectors/gene/gene-state.selector.ts
@@ -1,11 +1,19 @@
 // NgRx
-import { createSelector } from '@ngrx/store';
+import { createSelector, createSelectorFactory } from '@ngrx/store';
 // store
 import * as fromModule from '@gcv/gene/store/reducers';
 import { geneFeatureKey } from '@gcv/gene/store/reducers/gene.reducer';
+// app
+import { memoizeArray } from '@gcv/core/utils';
 
 
 export const getGeneState = createSelector(
   fromModule.getGeneModuleState,
   state => state[geneFeatureKey]
 );
+
+
+export const getLoading = createSelectorFactory(memoizeArray)(
+  getGeneState,
+  state => state.loading,
+);
diff --git a/client/src/app/gene/store/selectors/gene/selected-genes.selector.ts b/client/src/app/gene/store/selectors/gene/selected-genes.selector.ts
index 8eb8ff76..d715e95d 100644
--- a/client/src/app/gene/store/selectors/gene/selected-genes.selector.ts
+++ b/client/src/app/gene/store/selectors/gene/selected-genes.selector.ts
@@ -32,7 +32,7 @@ export const getUnloadedSelectedGeneIDs = createSelector(
   getSelectedGeneIDs,
   (state: State, ids: GeneID[]): GeneID[] => {
     const loadingIDs = new Set(state.loading.map(geneID));
-    const loadedIDs = new Set(state.loaded.map(geneID));
+    const loadedIDs = new Set(state.ids as string[]);
     const unloadedIDs = ids.filter((id) => {
         const idString = geneID(id);
         return !loadingIDs.has(idString) && !loadedIDs.has(idString);
diff --git a/client/src/app/gene/store/selectors/micro-tracks/clustered-and-aligned-micro-tracks.selector.ts b/client/src/app/gene/store/selectors/micro-tracks/clustered-and-aligned-micro-tracks.selector.ts
index d1364307..acf543a9 100644
--- a/client/src/app/gene/store/selectors/micro-tracks/clustered-and-aligned-micro-tracks.selector.ts
+++ b/client/src/app/gene/store/selectors/micro-tracks/clustered-and-aligned-micro-tracks.selector.ts
@@ -14,13 +14,13 @@ import { regexpFactory } from '@gcv/gene/algorithms/utils';
 import { Track } from '@gcv/gene/models';
 import { AlignmentParams, ClusteringParams } from '@gcv/gene/models/params';
 import { AlignmentMixin, ClusterMixin } from '@gcv/gene/models/mixins';
+import { familyCountMap } from '@gcv/gene/models/shims';
 
 
 // clustered
 
 
 // clusters micro tracks based on their families
-// TODO: update params to work with new clusterer
 // TODO: only cluster when selectedLoaded emits true
 export const getClusteredSelectedMicroTracks = createSelector(
   getSelectedMicroTracks,
@@ -38,12 +38,13 @@ export const getClusteredSelectedMicroTracks = createSelector(
       clusterfck.hcluster(tracks, metric, params.linkage, params.threshold);
     const recurrence = (cluster) => {
         const elements = [];
-        if ('left' in cluster || 'right' in cluster) {
-          if ('left' in cluster) {
+        if ('left' in cluster && 'right' in cluster) {
+          if (cluster['left']['size'] >= cluster['right']['size']) {
             elements.push(...recurrence(cluster['left']));
-          }
-          if ('right' in cluster) {
             elements.push(...recurrence(cluster['right']));
+          } else {
+            elements.push(...recurrence(cluster['right']));
+            elements.push(...recurrence(cluster['left']));
           }
         } else {
           elements.push(cluster['value']);
@@ -111,23 +112,44 @@ export const getClusteredAndAlignedSelectedMicroTracks = createSelector(
         // prepare the data
         const trackFamilies = tracks.map((t) => t.families);
         const l = trackFamilies[0].length;
-        const flattenedTracks = arrayFlatten(trackFamilies);
-        const characters = new Set(flattenedTracks);
+        const flattenedTracks: string[] = arrayFlatten(trackFamilies);
+        //const characters = new Set(flattenedTracks);
+        const familyCounts = familyCountMap(flattenedTracks);
+        const characters = new Set();
         const omit = new Set();
+        Object.entries(familyCounts).forEach(([family, count]) => {
+          if (count == 1 || family == '') {
+            omit.add(family);
+          } else {
+            characters.add(family);
+          }
+        });
         // construct and train the model
-        const hmm = new GCV.graph.MSAHMM(l, characters);
-        hmm.train(trackFamilies, {reverse: true, omit, surgery: true});
-        // align the tracks
-        const alignments = trackFamilies.map((f) => hmm.align(f));
-        const mixin = (t, i) => {
+        const mixinFactory = (alignments) => (t, i) => {
             const t2 = Object.create(t);
             t2.alignment = alignments[i];
             return t2;
           };
-        const alignedTracks = tracks.map(mixin);
-        const consensus = hmm.consensus();
-        accumulator.consensuses[i] = hmm.consensus();
-        accumulator.tracks.push(...alignedTracks);
+        // msa via hmm
+        if (characters.size > 0) {
+          const hmm = new GCV.graph.MSAHMM(l, characters);
+          hmm.train(trackFamilies, {reverse: true, omit});
+          // align the tracks
+          const alignments = trackFamilies.map((f,i) => {
+              return hmm.align(f, {inversions: false});
+            });
+          const alignedTracks = tracks.map(mixinFactory(alignments));
+          accumulator.consensuses[i] = hmm.consensus();
+          accumulator.tracks.push(...alignedTracks);
+        // edge case where all families are orphans or singletons
+        } else {
+          const alignments = trackFamilies.map((families) => {
+              return families.map((f, i) => i);
+            });
+          const alignedTracks = tracks.map(mixinFactory(alignments));
+          accumulator.consensuses[i] = [];
+          accumulator.tracks.push(...alignedTracks);
+        }
         return accumulator;
       };
     const clusteredAlignments = {
diff --git a/client/src/app/gene/store/selectors/router/index.ts b/client/src/app/gene/store/selectors/router/index.ts
index 90a0af43..c3a7e291 100644
--- a/client/src/app/gene/store/selectors/router/index.ts
+++ b/client/src/app/gene/store/selectors/router/index.ts
@@ -4,6 +4,8 @@ import { createSelector } from '@ngrx/store';
 import * as fromModule from '@gcv/gene/store/reducers';
 import { initialState } from '@gcv/gene/store/reducers/router.reducer';
 // app
+import { AppConfig } from '@gcv/app.config';
+import { arrayFlatten } from '@gcv/core/utils';
 import { AlignmentParams, BlockParams, ClusteringParams, QueryParams,
   SourceParams } from '@gcv/gene/models/params';
 import { instantiateAndPopulate } from '@gcv/gene/utils';
@@ -23,43 +25,21 @@ export const getParams = createSelector(
   (route) => route.state.params,
 );
 
-// TODO: get multi route genes too
 export const getRouteGenes = createSelector(
   getRouterState,
   (route): {name: string, source: string}[] => {
     // TODO: can this be handled upstream?
     if (route === undefined ||
         route.state === undefined ||
-        route.state.params === undefined ||
-        route.state.params.gene === undefined ||
-        route.state.params.source === undefined) {
+        route.state.params === undefined) {
       return [];
     }
+    const sources = AppConfig.SERVERS.map((s) => s.id);
     const params = route.state.params;
-    return [{name: params.gene, source: params.source}];
-  },
-);
-
-export const getSearchRoute = createSelector(
-  getRouterState,
-  // TODO: 'properly' set initial state
-  // https://github.com/ngrx/platform/issues/662
-  (route=initialState): {gene: string, source: string} => {
-    const params = route.state.params;
-    return {source: params.source, gene: params.gene};
-  },
-);
-
-export const getSearchRouteSource = createSelector(
-  getRouterState,
-  (route) => route.state.params.source,
-);
-
-export const getMultiRoute = createSelector(
-  getRouterState,
-  (route) => {
-    const params = route.state.params;
-    return {genes: params.genes};
+    const selectedGenes = sources
+      .filter((source) => source in params)
+      .map((source) => params[source].map((name) => ({source, name})));
+    return arrayFlatten(selectedGenes);
   },
 );
 
diff --git a/client/src/app/gene/store/utils/action-id.ts b/client/src/app/gene/store/utils/action-id.ts
new file mode 100644
index 00000000..dcf45a44
--- /dev/null
+++ b/client/src/app/gene/store/utils/action-id.ts
@@ -0,0 +1 @@
+export type ActionID = {action: number};
diff --git a/client/src/app/gene/store/utils/index.ts b/client/src/app/gene/store/utils/index.ts
index cddfaaf9..86b1b28e 100644
--- a/client/src/app/gene/store/utils/index.ts
+++ b/client/src/app/gene/store/utils/index.ts
@@ -1 +1,2 @@
+export * from './action-id';
 export * from './track-id';
diff --git a/client/src/app/gene/utils/custom-router-state-serializer.util.ts b/client/src/app/gene/utils/custom-router-state-serializer.util.ts
index 7bb9e524..112b9a61 100644
--- a/client/src/app/gene/utils/custom-router-state-serializer.util.ts
+++ b/client/src/app/gene/utils/custom-router-state-serializer.util.ts
@@ -1,5 +1,8 @@
+// Angular
 import { Params, RouterStateSnapshot } from '@angular/router';
 import { RouterStateSerializer } from '@ngrx/router-store';
+// app
+import { AppConfig } from '@gcv/app.config';
 import * as fromRouter from '@gcv/gene/store/reducers/router.reducer';
 
 // Returns an object including only the URL, params, and query params instead of
@@ -15,13 +18,15 @@ implements RouterStateSerializer<fromRouter.RouterStateUrl> {
     }
 
     let { url, root: { queryParams } } = routerState;
-    let { params } = route;
+    const params = Object.assign({}, route.params);
 
-    // convert route params into expected types
-    if (params.genes) {
-      params = Object.assign({}, params);
-      params.genes = params.genes.split(',');
-    }
+    // convert route params into expected types (gene lists)
+    const sources = AppConfig.SERVERS.map((s) => s.id);
+    sources.forEach((source) => {
+      if (source in params) {
+        params[source] = params[source].split(',');
+      }
+    });
 
     // convert route query params into expected types
     queryParams = Object.assign({}, queryParams);
diff --git a/client/src/assets/js/gcv/graph/msa-hmm.ts b/client/src/assets/js/gcv/graph/msa-hmm.ts
index 051e24e8..1e0ef71b 100644
--- a/client/src/assets/js/gcv/graph/msa-hmm.ts
+++ b/client/src/assets/js/gcv/graph/msa-hmm.ts
@@ -456,7 +456,7 @@ export class MSAHMM extends Directed {
         }
         while (reversePath[j].startsWith("d") && j >= 0) {
           if (reverse) {
-            path.push(reverse[j]);
+            path.push(reversePath[j]);
           }
           j--;
         }
@@ -610,7 +610,7 @@ export class MSAHMM extends Directed {
    */
   train(sequences,
         options: {
-          omit?: Set<any>,  // TODO: should omitting be left to the user?
+          omit?: Set<any>,
           reverse?: boolean,
           surgery?: boolean,
         }={})
@@ -618,7 +618,7 @@ export class MSAHMM extends Directed {
     // parse optional parameters
     this._setOption(options, "omit", new Set());
     this._setOption(options, "reverse", true);
-    this._setOption(options, "surgery", false);
+    this._setOption(options, "surgery", true);
     // train the model
     const filter = (sequence) => sequence.filter((s) => !options.omit.has(s));
     sequences.forEach((s, i) => {
@@ -668,7 +668,7 @@ export class MSAHMM extends Directed {
         }
         insertion = 0;
       };
-    let prev = "a";
+    let prev = "a0";
     let prevIndex = -1;
     for (let i = 1; i < path.length; i++) {
       const n = path[i];
@@ -688,6 +688,8 @@ export class MSAHMM extends Directed {
       } else if (n.startsWith("i")) {
         insertion++;
       }
+      prev = n;
+      prevIndex = n;
     }
     return alignment;
   }
@@ -714,19 +716,23 @@ export class MSAHMM extends Directed {
 
     // compute Viterbi paths and their emission probabilities
     let forward = sequence;
-    const forwardPath = this.viterbi(forward);
+    let forwardPath = this.viterbi(forward);
     let forwardEmissions = this.sequenceEmissions(forward, forwardPath);
     let reverse = (options.reverse || options.inversions) ?
       [...forward].reverse() : [];
-    const reversePath = this.viterbi(reverse);
+    let reversePath = this.viterbi(reverse);
     let reverseEmissions = this.sequenceEmissions(reverse, reversePath);
 
     // swap orientations depending on score
     const reversed =
       options.reverse && forwardPath.probability < reversePath.probability;
     if (reversed) {
-      [forward, forwardEmissions, reverseEmissions] =
-        [reverse, reverseEmissions, forwardEmissions];
+      [forward, reverse,
+      forwardPath, reversePath,
+      forwardEmissions, reverseEmissions] =
+        [reverse, forward,
+        reversePath, forwardPath,
+        reverseEmissions, forwardEmissions];
     }
 
     // compute inversions
@@ -740,8 +746,7 @@ export class MSAHMM extends Directed {
     // convert path to hmm state independent alignment
     let alignment = this.pathToAlignment(alignmentPath);
     if (reversed) {
-      const l = sequence.length-1;
-      alignment = alignment.map((x) => l-x);
+      alignment.reverse();
     }
 
     return alignment;
diff --git a/client/src/assets/js/gcv/metrics/levenshtein.ts b/client/src/assets/js/gcv/metrics/levenshtein.ts
index f7329055..6547cac7 100644
--- a/client/src/assets/js/gcv/metrics/levenshtein.ts
+++ b/client/src/assets/js/gcv/metrics/levenshtein.ts
@@ -1,17 +1,32 @@
-export const levenshtein = <T>(s: T[], t: T[]): number => {
-  const sLen = s.length;
-  const tLen = t.length;
-  return levenshteinRecurrence(s, sLen, t, tLen);
+import { matrix } from '../common';
+
+
+export const levenshtein = <T>(a: T[], b: T[]): number => {
+  const i = a.length;
+  const j = b.length;
+  const t = matrix(i+1, j+1, null);
+  return levenshteinRecurrence(a, i, b, j, t);
 }
 
-const levenshteinRecurrence = <T>(s: T[], sLen: number, t: T[], tLen: number): number => {
-  // base case: empty strings
-  if (sLen == 0) return tLen;
-  if (tLen == 0) return sLen;
-  // test if last characters of the strings match
-  let cost = (s[sLen-1] == t[tLen-1] ? 0 : 1);
-  // return minimum of delete char from s, delete char from t, and delete char from both
-  return Math.min(levenshteinRecurrence(s, sLen-1, t, tLen)+1,
-                  levenshteinRecurrence(s, sLen, t, tLen-1)+1,
-                  levenshteinRecurrence(s, sLen-1, t, tLen-1)+cost);
+
+const levenshteinRecurrence =
+<T>(a: T[], i: number, b: T[], j: number, t: number[]): number => {
+  // use memoized data if possible
+  if (t[i][j] === null) {
+    // base case: empty strings
+    if (i == 0) {
+      t[i][j] = j;
+    } else if (j == 0) {
+      t[i][j] = i;
+    // test if last characters of the strings match
+    } else {
+      let cost = (a[i-1] == b[j-1] ? 0 : 1);
+      // return minimum of delete char from a, delete char from b, and delete
+      // char from both
+      t[i][j] = Math.min(levenshteinRecurrence(a, i-1, b, j, t)+1,
+                         levenshteinRecurrence(a, i, b, j-1, t)+1,
+                         levenshteinRecurrence(a, i-1, b, j-1, t)+cost);
+    }
+  }
+  return t[i][j];
 }