diff --git a/src/components/workspace/uploadworkspace/settings.jsx b/src/components/workspace/uploadworkspace/settings.jsx
index d7762c0..2e0375e 100644
--- a/src/components/workspace/uploadworkspace/settings.jsx
+++ b/src/components/workspace/uploadworkspace/settings.jsx
@@ -10,29 +10,33 @@ const SettingsPanel = ({ onLogoTypeChange, onScaleChange, onStartPosChange,
 			 onModeChange, mode, logodefault, scaledefault,
 			 startposdefault, alphabet, onAlphabetUpdate, onFrequencyChange,
                          backgroundFrequencies, onApplyToFile, onApplyToAll, yAxisAuto,
-                         onYAxisToggle, yAxisMax }) => (
+                         onYAxisToggle, yAxisMax, hasNegatives }) => (
 			     <Menu vertical style={{ width: '100%', backgroundColor: "#fafafa" }}>
-			       <Menu.Item>
-				 <ModeDropdown header="Letter height"
-					       onChange={onModeChange}
-                                               onFrequencyChange={onFrequencyChange}
-                                               backgroundFrequencies={backgroundFrequencies}
-                                               mode={mode} />
-			       </Menu.Item>
-                               { mode !== FREQUENCY && (
-                                   <Menu.Item>
-                                     <Header as="h3">y-axis maximum</Header>
-                                     <Form>
-                                       <Form.Field>
-                                         <Radio label="auto" checked={yAxisAuto} onClick={() => onYAxisToggle(true, yAxisMax)} />
-                                       </Form.Field>
-                                       <Form.Field>
-                                         <Radio onClick={() => onYAxisToggle(false, yAxisMax)} checked={yAxisAuto === false} />&nbsp;
-                                         <Input maxLength={5} value={("" + yAxisMax).substring(0, 5) + (yAxisMax === Math.floor(yAxisMax) ? '.' : "")} onChange={e => onYAxisToggle(false, +e.target.value)} style={{ width: "70%" }} size="mini" />
-                                       </Form.Field>
-                                     </Form>
-                                     
-                                   </Menu.Item>
+                               { !hasNegatives && (
+                                   <React.Fragment>
+			             <Menu.Item>
+				       <ModeDropdown header="Letter height"
+					             onChange={onModeChange}
+                                                     onFrequencyChange={onFrequencyChange}
+                                                     backgroundFrequencies={backgroundFrequencies}
+                                                     mode={mode} />
+			             </Menu.Item>
+                                     { mode !== FREQUENCY && (
+                                         <Menu.Item>
+                                           <Header as="h3">y-axis maximum</Header>
+                                           <Form>
+                                             <Form.Field>
+                                               <Radio label="auto" checked={yAxisAuto} onClick={() => onYAxisToggle(true, yAxisMax)} />
+                                             </Form.Field>
+                                             <Form.Field>
+                                               <Radio onClick={() => onYAxisToggle(false, yAxisMax)} checked={yAxisAuto === false} />&nbsp;
+                                               <Input maxLength={5} value={("" + yAxisMax).substring(0, 5) + (yAxisMax === Math.floor(yAxisMax) ? '.' : "")} onChange={e => onYAxisToggle(false, +e.target.value)} style={{ width: "70%" }} size="mini" />
+                                             </Form.Field>
+                                           </Form>
+                                           
+                                         </Menu.Item>
+                                     )}
+                                   </React.Fragment>
                                )}
                                <Menu.Item>
                                  <ColoredInput header="Starting base number" defaultValue={startposdefault || 1} onChange={onStartPosChange} />
@@ -42,8 +46,8 @@ const SettingsPanel = ({ onLogoTypeChange, onScaleChange, onStartPosChange,
 			       </Menu.Item>
                                <Menu.Item>
                                  <Header as="h3">Apply these settings to...</Header>
-			         <Button onClick={() => window.confirm(CONFIRM) && onApplyToFile && onApplyToFile()}>all motifs in the current file</Button><br/><br/>
-                                 <Button onClick={() => window.confirm(CONFIRM) && onApplyToAll && onApplyToAll()}>all loaded motifs</Button>
+			         <Button onClick={() => window.confirm(CONFIRM) && onApplyToFile && onApplyToFile(hasNegatives, mode)}>all motifs in the current file</Button><br/><br/>
+                                 <Button onClick={() => window.confirm(CONFIRM) && onApplyToAll && onApplyToAll(hasNegatives, mode)}>all loaded motifs</Button>
 			       </Menu.Item>
 			     </Menu>
 			 );
diff --git a/src/components/workspace/uploadworkspace/uploadworkspace.jsx b/src/components/workspace/uploadworkspace/uploadworkspace.jsx
index 84eee6d..7f27554 100644
--- a/src/components/workspace/uploadworkspace/uploadworkspace.jsx
+++ b/src/components/workspace/uploadworkspace/uploadworkspace.jsx
@@ -1,6 +1,6 @@
 import React from 'react';
 import { Grid, Menu, Dropdown, Button, Icon } from 'semantic-ui-react';
-import { embedLogo, Logo, INFORMATION_CONTENT } from 'logosj-react';
+import { embedLogo, Logo, INFORMATION_CONTENT, LogoWithNegatives } from 'logosj-react';
 
 import { _svgdata } from '../../svgdownload/utils';
 import SVGZip from '../../../utilities/zipfile';
@@ -42,12 +42,14 @@ class UploadWorkspace extends React.Component {
 	};
     }
 
-    _updateFile() {
+    _updateFile(hasNegatives, mode) {
         const nLogo = {
             startpos: this.state.selected.startpos,
-            alphabet: this.state.selected.alphabet,
-            backgroundFrequencies: this.state.selected.backgroundFrequencies
+            alphabet: this.state.selected.alphabet
         };
+        if (!hasNegatives) nLogo.backgroundFrequencies = this.state.selected.backgroundFrequencies;
+        if (!hasNegatives) nLogo.mode = mode;
+        if (!hasNegatives && mode === INFORMATION_CONTENT) nLogo.yAxisMax = this.state.selected.yAxisAuto === false ? this.state.selected.yAxisMax : null;
         const nSets = [ ...this.state.logoSets ];
         const nLogos = this.state.selectedFile.logos.map( logo => ({
             ...logo,
@@ -65,12 +67,14 @@ class UploadWorkspace extends React.Component {
         });
     }
 
-    _updateAll() {
+    _updateAll(hasNegatives, mode) {
         const nLogo = {
             startpos: this.state.selected.startpos,
-            alphabet: this.state.selected.alphabet,
-            backgroundFrequencies: this.state.selected.backgroundFrequencies
+            alphabet: this.state.selected.alphabet
         };
+        if (!hasNegatives) nLogo.backgroundFrequencies = this.state.selected.backgroundFrequencies;
+        if (!hasNegatives) nLogo.mode = mode;
+        if (!hasNegatives && mode === INFORMATION_CONTENT) nLogo.yAxisMax = this.state.selected.yAxisAuto === false ? this.state.selected.yAxisMax : null;
         const nSets = [ ...this.state.logoSets ];
         nSets.forEach( (logoSet, i) => {
             const nLogos = logoSet.logos.map( logo => ({
@@ -292,12 +296,27 @@ class UploadWorkspace extends React.Component {
             yAxisMax
         });
     }
+
+    _hasNegatives(ppm) {
+        let r = false;
+        ppm.forEach( row => { row.forEach( x => { if (x < 0) r = true; } ); } );
+        return r;
+    }
     
     render() {
+        
         let isdone = this.state.remaining === 0 && this.state.logoSets.length > 0;
         let selectedPPMs = this.state.selectedFile && this.state.selectedFile.logos;
         const selectedProps = this.state.selected ? { ...this.state.selected } : {};
         if (selectedProps && selectedProps.yAxisAuto) selectedProps.yAxisMax = null;
+        
+        const defaultMax = this.state.selected && (
+            this.state.selected.backgroundFrequencies
+                ? Math.max(...this.state.selected.backgroundFrequencies.map( x => Math.log2(1.0 / (x || 0.01))))
+                : (this.state.selected.alphabet && Math.log2(this.state.selected.alphabet.length))
+        );
+        const hasNegatives = this.state.selected && this.state.selected.ppm && this._hasNegatives(this.state.selected.ppm);
+        
 	return (
 	    <React.Fragment>
 	      <PasteModal open={this.state.pasteModalShown} onClose={this.pasteModalClosed.bind(this)} />
@@ -307,6 +326,7 @@ class UploadWorkspace extends React.Component {
                   { this.state.selected && (
                       <Grid.Column width={3}>
                         <SettingsPanel
+                          hasNegatives={hasNegatives}
                           onApplyToFile={this._updateFile.bind(this)}
                           onApplyToAll={this._updateAll.bind(this)}
                           onStartPosChange={this._startPosChange.bind(this)}
@@ -317,8 +337,8 @@ class UploadWorkspace extends React.Component {
                           backgroundFrequencies={this._backgroundFrequencyMap()}
                           onFrequencyChange={this._backgroundUpdate.bind(this)}
                           onAlphabetUpdate={this._alphabetUpdate.bind(this)}
-                          yAxisAuto={this.state.selected.yAxisAuto !== false}
-                          yAxisMax={this.state.selected.yAxisMax || Math.max(...this.state.selected.backgroundFrequencies.map( x => Math.log2(1.0 / (x || 0.01)) ))}
+                          yAxisAuto={this.state.selected && this.state.selected.yAxisAuto !== false}
+                          yAxisMax={(this.state.selected && this.state.selected.yAxisMax) || defaultMax}
                           onYAxisToggle={this._yAxisToggle.bind(this)}
                         />
                       </Grid.Column>
@@ -385,7 +405,13 @@ class UploadWorkspace extends React.Component {
                           <div ref={this.hiddenLogo} style={{ display: "none" }} />
                           <div ref={this.logo}
                                style={{ maxHeight: "500px", height: "20%", textAlign: "center" }}>
-                            { isdone && (<Logo {...selectedProps} width="90%" height="100%" />)}
+                            { isdone && (
+                                hasNegatives ? (
+                                    <LogoWithNegatives values={this.state.selected.ppm} {...selectedProps} width="90%" height="100%" />
+                                ) : (
+                                    <Logo {...selectedProps} width="90%" height="100%" />
+                                )
+                            )}
                           </div>
                           <div style={{ maxHeight: "500px", height: "30%", textAlign: "center" }}>
                             <WorkspaceEditorTabs