CodonCode Aligner User Manual CodonCode Aligner User Manual Table of Contents About CodonCode Aligner.................................................................................................................................1 System Requirements..............................................................................................................................1 Licenses....................................................................................................................................................1 Licenses for CodonCode Aligner.......................................................................................................................3 Demo Mode.............................................................................................................................................3 Time-limited Trials..................................................................................................................................3 Single-user Licenses................................................................................................................................4 Using Phred and Phrap from CodonCode Aligner............................................................................4 Replacement License Keys...............................................................................................................5 License Server Licenses...........................................................................................................................5 Firewall ports for License Server use................................................................................................6 CodonCode Aligner Features.............................................................................................................................7 Aligner Windows and Views..................................................................................................................7 The Main Window.............................................................................................................................7 Project Window.................................................................................................................................8 Base View Window...........................................................................................................................8 Trace Window..................................................................................................................................9 Quality View Window.....................................................................................................................10 Contig View Window......................................................................................................................10 Restriction Map Window................................................................................................................11 Customizable Toolbars..........................................................................................................................12 Regions of Interest.................................................................................................................................12 Take the Quick Tour!.............................................................................................................................13 Usage Tips for CodonCode Aligner.................................................................................................................14 Quality Values In CodonCode Aligner...........................................................................................................15 Quality values explained........................................................................................................................15 Where quality values come from...........................................................................................................15 Artificial qualities..................................................................................................................................16 Gap qualities..........................................................................................................................................16 Viewing qualities...................................................................................................................................16 Additional Reading................................................................................................................................17 Aligner Projects.................................................................................................................................................18 Working with Aligner Projects........................................................................................................................20 Creating New Projects...........................................................................................................................20 Opening Existing Projects.....................................................................................................................21 Saving Projects......................................................................................................................................21 Closing Projects.....................................................................................................................................21 Adding Sample Files to Aligner Projects........................................................................................................22 Opening Single Sample Files.................................................................................................................22 Adding Several Sample Files.................................................................................................................22 Adding a Subset of Samples..................................................................................................................23 i CodonCode Aligner User Manual Table of Contents Adding Sample Files to Aligner Projects Adding Entire Folders of Sample Files..................................................................................................24 Adding Entire Assemblies.....................................................................................................................24 Importing Sequencher Projects (CAF Files)...................................................................................25 Importing Phrap Assemblies...........................................................................................................26 Tags in Phrap assemblies................................................................................................................26 Import from GenBank............................................................................................................................26 Creating new text sequences..................................................................................................................27 Compatible File Formats.......................................................................................................................28 Sample Names.......................................................................................................................................29 Organizing Samples And Contigs In Folders.................................................................................................31 Creating Folders.....................................................................................................................................31 Moving Samples and Contigs to Folders...............................................................................................31 Renaming Folders..................................................................................................................................31 Deleting Folders.....................................................................................................................................31 Removing Samples from an Aligner Project..................................................................................................33 Base Calling with PHRED................................................................................................................................34 How to call bases with PHRED from Aligner.......................................................................................34 Prerequisites....................................................................................................................................34 What Aligner does...........................................................................................................................35 Editing the PHRED parameter file........................................................................................................35 Base calling problems............................................................................................................................37 Cannot find base calling program...................................................................................................37 Missing entries in the Phred parameter file.....................................................................................38 Problems reading the Phred parameter file.....................................................................................39 .........................................................................................................................................................39Wrong