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Sequencher 5.4.6 is Released!

October 13,2016

New and enhanced features for all of your DNA sequence analysis.

Sanger:

  • Send primer pair sequences from Primer-BLAST runs in Sequencher Connections to your Sequencher project.
  • Easily use consensus sequences from the Project Window as a reference sequence for NGS alignments for hybrid sequencing projects.
  • New Batch Revert Trim Ends command.
  • Ability to adjust the font size in the Project Window. 

NGS:

  • Faster GSNAP and BWA-MEM workflows.
  • Build GSNAP Databases and BWA Indexes that can be re-used for aligning to whole genomes.
  • View and save quality scores and metadata of your NGS raw data files with FastQC reports.
  • Generate Variant Calling Files (VCF) to flag variants in your NGS alignments using SAMtools.

RNA-Seq:

  • Expanded Cufflinks suite with the addition of Cuffquant and Cuffnorm.
  • A unique Conditions and Replicates Editor for Cuffdiff and Cuffnorm.
  • Enhanced RNA-Seq visualizations with custom sorting and filtering options.   
  • Easily manage all of your DNA-Seq and RNA-Seq projects with an enhanced External Data Browser.

CodeLinker 1.0 is now available!

August 26,2016

Gene Codes announces the release of CodeLinker 1.0, software for the analysis of RNA-Seq and microarray data.

With CodeLinker, you can choose to analyze your data with a number of different clustering algorithms. You can then visualize the cluster data with a variety of plots. CodeLinker also features Self-Organizing Maps (SOM's) and Principle Component Analysis (PCA)

CodeLinker also brings you prediction tools that allow you to search your data for associations and then apply those associations to new samples. You can use Sub-Linear Association Mining (SLAM) to search your data for associations and then use the associations to train an Artificial Neural Network (ANN). You can also explore your data with an Integrated Bayesian Inference System (IBIS) classifier to find patterns of gene expression, and then use those patterns to perform Discriminant Analysis. 

Sequencher 5.4.5 is Available Now!

June 23,2016

New features for Sanger and Next-Generation DNA Sequence Analysis include:

Sanger: 

  • New Batch Revert Trim Ends command.
  • Ability to adjust the font size in the Project Window.  
  • For hybrid sequencing projects, you can create NGS reference databases/indexes directly from the consensus sequences in the Project Window in addition to linking to an external sequence.

NGS:

  • GSNAP and BWA-MEM workflows now produce BAM files. 
  • Enhancements to the External Data Browser (EDB).  
  • FastQC Reports now open automatically.

Sequencher 5.4.1 is Released!

December 18,2015

Gene Codes announces the release of Sequencher 5.4.1.  This new release adds features to Sanger and NGS such as:

  • Build GSNAP Databases and BWA Indexes that can be re-used and persisted with your project.
  • Sequencher is able to handle larger genomes when aligning sequences using GSNAP and BWA.
  • An updated External Data Browser that now includes a Final Run Status column that will report statuses of SUCCESS and FAILED.
  • An updated External Data Browser that includes run results for new DNA-Seq options for GSNAP Databases and BWA Indexes.
  • Sequencher Connections now offers the ability to send primer pair sequences returned from a Primer-BLAST run to your Sequencher project.
  • Primer sequences sent to your Sequencher project from Sequencher Connections have colored bases and primer features applied to them.

Sequencher 5.4 is now available!

September 21,2015

Gene Codes announces the release of Sequencher 5.4.  This new release adds features to Sanger, NGS and RNA-Seq analyses such as:

  • Expanded Cufflinks suite with the addition of Cuffquant and Cuffnorm.  Sequencher 5.4 also has replicates functionality with a unique Conditions and Replicates Editor for Cuffdiff and Cuffnorm.
  • Enhanced RNA-Seq visualizations with custom sorting and filtering options.
  • View and save quality scores and metadata of your NGS raw data files with FastQC reports.
  • Generate Variant Calling Files (VCF) to flag variants in your NGS alignments using SAMtools.
  • Updated version of GSNAP which runs faster and has additional alignment modes.
  • An updated External Data Browser for organizing both DNA-Seq and RNA-Seq projects.
  • Sequencher Connections has improved organization and usability.

Sequencher 5.3 is now available!

December 18,2014

Gene Codes announces the release of Sequencher 5.3.  We continue to add more features for Sanger and NGS users including:

  • The Cufflinks suite for RNA-Seq data ÔÇô Our user-friendly interface gives you the power of the command line without the hassle of the command line.
  • Visualization tools for Differential Expression analysis.
  • Enhancements to Sequencher Connections ÔÇô Our visionary tool for running multiple analyses in parallel is now more flexible and customizable. 

Sequencher 5.2.4 is Available!

February 21,2014

Gene Codes is proud to announce the release of our most flexible version of Sequencher ever!  Sequencher 5.2.4 combines support for all licensing options whether it's standalone or network, dongle or keyless. 

Network customers using KeyServer now have access to all the latest features:

  • Sequencher Connections - A whole new way to accelerate your analysis!  Perform multiple customized BLAST searches or MUSCLE alignment on single or groups of sequences.  View your results in webpage, text, or XML format all without leaving Sequencher!
  • Use MUSCLE to create phylogenetic trees that can be viewed in multiple formats.
  • BWA reference-guided alignment algorithm for NGS data sets.
  • Added GSNAP flexibility - You now have the ability to capture reads that didn't align, or even to select only reads that didn't align. 

Sequencher 5.2.3 with new Sequencher Connections is Available Now!

October 15,2013
  • Downloadable Upgrade
  • Software license (dongle-free) options
  • BWA-MEM algorithm for NGS    
  • Our Visionary New Tool for Sanger and NGS data -- Sequencher Connections
  • Faster, Powerful, and Easy to Use!

Sequencher 5.1 is Available Now!

November 16,2012

Gene Codes announces the release of Sequencher 5.1 DNA analysis software for Sanger or NGS data sets. Some of the new features include:

  • De Novo Alignment for NGS data
  • Multiplex ID Assembly
  • A new sequence alignment algorithm for Sanger data
  • A protein searching feature for any type of DNA sequence data

Sequencher 5.0.1 for Mac OSX (Lion) has been released.

January 12,2012

Macintosh OS X Lion Compatibility is coming soon.

August 22,2011

A new Macintosh version of Sequencher fully compatible with Apple's OS 10.7 (Lion) will begin beta-testing in September. Keep checking our website or follow us on Facebook, LinkedIn and Twitter for updates on the final release schedule.

Gene Codes’ Sequencher 5.0 Delivers Next-generation DNA Sequence Analysis

June 27,2011

Gene Codes Corporation announces the release of Sequencher 5.0. It incorporates new DNA sequence data alignment algorithms with SNP and methylation analysis for next-generation DNA sequence data. Performance for assembly and alignment of sequences and contigs is hundreds of times faster. New alignment functions and database searching features make getting reliable results from both capillary electrophoresis and next-generation data faster than ever.

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