Sequencher

Sequencher is the industry standard software for DNA sequence analysis. It works with all automated sequencers and is widely known for its lightning-fast contig assembly, short learning curve, user-friendly editing tools, and superb technical support. First released almost 15 years ago, Sequencher is currently used for sequence analysis tasks in every major genomic and pharmaceutical company as well as numerous academic and government labs in over 40 countries around the world. Life Science researchers use Sequencher for many diverse DNA sequence analysis applications including de novo gene sequencing, mutation detection, forensic human identification, systematics, and more.

Sequencher capabilities include heterozygote and SNP detection and analysis, cDNA to Genomic DNA large gap alignment, comparative sequencing, support for confidence scores, ORF translation, GenBank feature import, and restriction enzyme mapping. It has many new capabilities that can reduce the time required to identify and validate heterozygotes and SNPs in your sequences.

Pricing for Sequencer must be obtained by requesting a quote, which you can do here.

What's New

• RNA-Seq Differential Expression with Cufflinks Suite - You can now perform Differential Expression in Sequencher using Cufflinks.
• New RNA-Seq Tools Installer - We have created a single downloadable installer to add all the components you need to perform RNA-Seq analysis.
• Cufflinks, Cuffmerge, and Cuffdiff Added to External Data Browser - We have extended the External Data Browser so that you can manage and annotate your RNA-Seq runs.
• Cufflinks - You can now assemble RNA-Seq reads into transcripts from SAM or BAM files using Cufflinks.
• Cufflinks Advanced Options - Sequencher gives you access to all of the Cufflinks command line options through its innovative GUI.
• Cuffmerge - You can merge Cufflinks assemblies using Cuffmerge prior to performing Differential Expression analysis.
• Cuffdiff - Cuffdiff performs the analyses and statistical tests to find significant changes in expression, splicing, and promotor usage.
• Cuffdiff Advanced Options - Sequencher gives you access to all of Cuffdiff's command line options through its innovative GUI.
• Viewing Interim Cufflinks Data and Plots - Explore your interim Cufflinks genes.fpkm_tracking and isoforms.fpkm_tracking files using the new Bar Chart with links to the underlying data.
• Viewing Cuffdiff Differential Expression Data and Plots - View the results of your RNA-Seq Differential Expression analysis as Volcano, Scatter, or Bar charts. Click on a bar or spot to see the underlying data highlighted.
• Sequencher Connections Completely Rewritten - You can now open more than one Connections Session of the same type at a time. Sessions are saved and you may open saved Sessions at any time.
• New Sequencher Connections Menu Items - The existing menu commands for adding sequences to Sequencher Connections have been replaced with two new menu items for adding sequences to a Session or opening an existing Session.
• Introducing The Session Launcher - The new Sequencher Connections Session Launcher allows you to add and name new Sessions, list saved Sessions, and choose a Session to add more data to.
• Viewing Historic Sessions - Sequencher automatically saves the results of any Connections Session and lets you view the results at a later date.
• Adding more sequences to an existing Session - You can now add more sequences to an existing Individual Connections Session or another group of sequences to an existing Group Session.
• Duplicate Names Warning for Group Sessions - Connections warns you if you try to add sequences with the same name to a Group Session and asks you to rename them.
• Session Jobs Still Running Warning - If you try to quit Sequencher while there are still Sessions running, you will get a warning and will be asked if you want to quit or keep the Sessions running.
• Invalid Data Warning - Sequencher lets you know if there is a problem with data in an existing Session when you try to run a new search.
• Results Have Expired from NCBI Website Warning - Results expire from the NCBI website after 36 hours. You will see a warning in your Connections Session Web View, but since your results are saved, you can still see them in Connections.
• Too Many Sequences in Session - Each Individual Session has a limit of 384 sequences. If you try to add more than this in one Session, you will get a warning asking you to try with fewer sequences.
• Too Much Data Being Sent to Connections - There is a limit of 15,000,000 bases per Session, you will be warned if your single sequence or combination of sequences exceeds this limit.

What's Improved

• Improved Compliance with BLAST Queueing Rules - We have improved our compliance with the rules that NCBI BLAST imposes for load management of searches.
• Three New Insert Channel Before Commands - We have added three new right-click menu items to improve your Connections workflow, these are Insert BLAST Channel Before, Insert Primer-BLAST Channel Before, and Insert Local-BLAST Channel Before. These three new menu items replace the old Insert Channel Before menu item.
• Display BLAST and Primer-BLAST on Same Schematic - You can now display BLAST and Primer-BLAST results on the same Schematic.
• Local-BLAST Has its Own Channel Options - We have made Local-BLAST a separate Channel with its own Channel Options to make it easier to use with BLAST and Primer-BLAST.
• Sequencher is OS X 10.10 Yosemite Compatible - Sequencher is compatible with Apple's Yosemite (OS X 10.10) operating system.