Geneious Prime 2019.2 User Manual Biomatters Ltd September 24, 2019 Contents 1 Getting Started7 1.1 Downloading & Installing Geneious Prime ..................... 7 1.2 Geneious Prime setup ................................. 9 1.3 Upgrading to new versions .............................. 16 1.4 Licensing......................................... 17 1.5 Troubleshooting..................................... 19 2 The Geneious Prime Main Window 21 2.1 The Sources Panel.................................... 22 2.2 The Document Table .................................. 22 2.3 The Document Viewer Panel.............................. 25 2.4 The Toolbar ....................................... 26 2.5 The Help Panel ..................................... 27 2.6 Geneious Prime menu bar options .......................... 29 3 Importing and Exporting Data 35 3.1 Importing data from the hard drive to your Local folders............. 35 3.2 Data input formats ................................... 36 3.3 Importing files from public databases ........................ 44 3.4 Agents .......................................... 47 3.5 Exporting files...................................... 50 3.6 Printing and Saving Images.............................. 52 4 Managing Your Local Documents 55 4.1 Organizing your local documents........................... 55 4.2 Searching and filtering local documents....................... 58 4.3 Find Duplicates..................................... 62 4.4 Batch Rename...................................... 63 4.5 Backing up your local documents........................... 63 4.6 Document History ................................... 65 5 Creating, Viewing and Editing Sequences 67 5.1 Creating new sequences ................................ 67 5.2 The Sequence Viewer.................................. 69 5.3 Customizable text view for sequences ........................ 81 2 CONTENTS 3 5.4 Editing sequences.................................... 82 5.5 Complement and Reverse Complement ....................... 84 5.6 Translating sequences.................................. 85 5.7 Viewing chromatograms................................ 86 5.8 Meta-data ........................................ 88 6 Parent / Descendant Tracking 93 6.1 Editing Linked Documents............................... 94 6.2 The Lineage View.................................... 96 7 RNA, DNA and Protein Structure Viewer 99 7.1 RNA/DNA secondary structure fold viewer .................... 99 7.2 3D protein structure viewer ..............................100 8 Working with Annotations 103 8.1 Viewing, editing and extracting annotations.....................103 8.2 Adding annotations...................................108 8.3 Compare Annotations .................................113 9 Sequence Alignments 117 9.1 Dotplots .........................................117 9.2 Sequence Alignments..................................119 9.3 Alignment viewing and editing............................126 9.4 Alignment masking...................................131 9.5 Consensus sequences..................................132 10 Assembly and Mapping 135 10.1 Supported sequencing platforms ...........................135 10.2 Read processing.....................................136 10.3 De novo assembly....................................146 10.4 Map to reference.....................................149 10.5 Viewing Contigs.....................................156 10.6 Editing Contigs .....................................158 10.7 Extracting the Consensus................................159 11 Analysis of Assemblies and Alignments 161 11.1 Finding polymorphisms ................................161 11.2 Analyzing Expression Levels .............................164 12 Building Phylogenetic Trees 177 12.1 Phylogenetic tree representation ...........................177 12.2 Tree building in Geneious Prime ...........................178 12.3 Tree building methods and models..........................181 12.4 Resampling – Bootstrapping and jackknifing ....................183 12.5 Viewing and formatting trees .............................185 4 CONTENTS 13 Primers 189 13.1 Design New Primers ..................................189 13.2 Manual primer design .................................198 13.3 Importing primers from a spreadsheet........................200 13.4 Primer Database.....................................201 13.5 Test with Saved Primers ................................202 13.6 Add Primers to Sequence................................203 13.7 Characteristics for Selection ..............................204 13.8 Convert to Oligo.....................................204 13.9 Primer Extensions....................................205 13.10 Extract PCR Product ..................................205 13.11 More Information....................................207 14 Cloning 209 14.1 Find Restriction Sites..................................209 14.2 Digest into fragments..................................212 14.3 Creating a custom enzyme set.............................215 14.4 Introduction to the cloning interface .........................216 14.5 Restriction Cloning...................................218 14.6 Golden Gate.......................................219 14.7 Gibson Assembly....................................221 14.8 Gateway® Cloning ...................................223 14.9 TOPO® Cloning.....................................224 14.10 Copy-paste cloning...................................225 14.11 CRISPR site finder....................................225 14.12 Analyze Silent Mutations................................228 14.13 Optimize Codons....................................229 15 BLAST 233 15.1 Setting up a BLAST search...............................233 15.2 BLAST results......................................235 15.3 NCBI BLAST.......................................237 15.4 Adding alternative BLAST server locations .....................239 15.5 Custom BLAST .....................................239 16 Workflows 245 16.1 Managing Workflows..................................245 16.2 Creating and editing Workflows............................246 16.3 Custom code in Workflows ..............................250 17 Geneious Education 251 17.1 Creating a tutorial....................................251 17.2 Answering a tutorial ..................................252 18 Saving Operation Settings (Option Profiles) 253 CONTENTS 5 19 Shared Databases 255 19.1 Using a Shared Database................................255 19.2 Direct SQL Connection.................................259 19.3 Geneious Server Database...............................267 20 Geneious Server 275 20.1 Introduction to Geneious Server............................275 20.2 Accessing Geneious Server...............................275 20.3 Running jobs and retrieving results..........................277 20.4 Geneious Server enabled plugins...........................279 21 Advanced Administration 281 21.1 Default data location ..................................281 21.2 Change default preferences ..............................282 21.3 Pre-configuring Shared Database connections....................283 21.4 Pre-configuring license server location........................283 21.5 Deleting built-in plugins................................283 21.6 Max memory.......................................284 21.7 Web Linking to Data in Geneious Prime.......................284 6 CONTENTS Chapter 1 Getting Started The best way to get started with Geneious Prime is to try out some of our tutorials. The Tutorial option under the Help menu provides an inbuilt tutorial with a basic introduction to the major features of Geneious Prime. Additional tutorials on specialized functions can be downloaded from our website https://www.geneious.com/tutorials. For additional information and help with troubleshooting, please visit the Geneious support website at https://support.geneious.com. 1.1 Downloading & Installing Geneious Prime Geneious Prime is free to download from https://www.geneious.com/download. If you are a first-time user you will be offered a free trial. If you have already purchased a license you can enter it when Geneious Prime starts up. To download the latest version of Geneious Prime, click on https://www.geneious.com/ download (or type it in to your internet browser), choose the version you want to download and click Download. If you have a 64-bit Linux or Windows machine, ensure you check the “64-bit” box. Geneious Prime can be run on Windows, Mac, or Linux. The following OS versions are sup- ported: Operating System Version Windows 7/8/10 Mac OS 10.8 - 10.14 Linux CentOS or RHEL 6 or higher/Ubuntu Desktop LTS, last 2 supported versions 7 8 CHAPTER 1. GETTING STARTED We recommend at least the following specifications for running Geneious Prime (note that these are minimum requirements - for working with large datasets such as NGS sequences you will need a higher-spec machine): • Processor: Intel x86/x86 64 • Memory: 2048MB or more • Hard-disk: 2GB or more free space • Video: 1024x768 resolution or higher Geneious Prime comes bundled with the correct version of Java for your OS. If you require a version that does not include Java, please contact Geneious Support. Installing on Windows Download the installer for Windows, then double-click on it to run it and follow the prompts. The default installation location is in Program Files. Installing on macOS Download the installer for macOS. If the disk image does not automatically open, double-click on it to open it. Drag the Geneious icon to Applications