Partek® Genomics Suite® Updates

The Partek Updates repository provides links and details regarding current Partek software releases. If you are not running the current build, you can update by downloading and installing the newest release from the Software Downloads tab.

To identify which release you currently have installed, follow these steps:

  • Windows and Linux: Go to the Help menu within Partek Genomics Suite and select About Partek Genomics Suite
  • Macintosh: Go to the About Partek Genomics Suite menu and select About Partek Genomics Suite

For more information, please contact Partek Licensing.

Windows 32-bit
(Windows 7, 8, 10)
Windows 64-bit
(Windows 7, 8, 10)
Mac (32-bit) - Snow Leopard (10.6) & Lion/Mountain Lion (10.7/10.8)* Mac (64-bit) - El Capitan (10.11), Yosemite (10.10), & Mavericks (10.9)* Linux 64-bit**
Partek Genomics Suite 6.6
April 19, 2016

April 19, 2016

February 20, 2014

April 19, 2016

April 19, 2016

*If you are using a Mac and connecting to a server, please review the special instructions under the License FAQ tab above.

**Instructions for installing Partek on Linux are here.

Features and Improvements

Partek Genomics Suite 6.6 Release Notes

    • Improved importing GSA projects downloaded from Partek Flow output for alt-splicing analysis
    • Improved Illumina EPIC chip importing
    • Improved quantile normalization on a selected categorical column by giving a clearer message
    Bug fixes:
    • Fixed a bug on finding miRNA in the TargetScan database link
    • Fixed a bug where power analysis dialog went behind the main window
    • Fixed a bug on logistic regression file saving dialog
    • Fixed a bug on sample QC step on LOH workflow
    • Other minor bug fixes

    • Improved the installation process
    • Improved text file import which containse non-ASCII characters
    • Changed the Q1 and Q3 calculation to use the same method ( method 2
    • Improved power analysis graph display axis labeling
    Bug fixes:
    • Fixed a bug on standardization calculation
    • Fixed a bug on interactive filter function
    • Fixed a bug on power analysis dialog crash
    • Other minor bug fixes

    • Added support for Illumina Infinium MethylationEPIC arrays
    Bug fixes:
    • Minor bug fixes

    • Improved the speed of insert annotation
    • Removed Order Taqman assays from gene expression workflow
    Bug Fixes:
    • Fixed a bug on HTS import error when there is only one plate
    • Other minor bug fixes

    • Improvement of visualization on Mac
    • Improvement on BCF/VCF import to include filter field
    • Added annotation steps on Illumina bead array methylation workflow
    • Added Fluidigm copy number data importer
    • Added import option on gz format of vcf file
    Bug Fixes:
    • Minor bug fixes

    • Change the default unsaved pathway enrichment result to temp directory
    • Add more options to output gene list when select a pathway in pathway enrichment result
    • Add number of observation option in column statistics when group by a categorical column
    • Add output allele base information when create allele specific copy number
    • Improvement on Fluidigm importer when there are missing values
    • Improvement on display non-English characters in spreadsheet
    Bug Fixes:
    • Bug fixes on hierarchical clustering

    • Changed the default of Aglient miRNA feature extract to gTotalSignal
    • Add column label display text length option in hierarchical cluster
    Bug Fixes:
    • Fixed a bug on model selection using nearest centroid posterior probability report

    • Added more options on Illumina IDAT importer
    • Added extension name (.prd) automatically when saving distribution file
    • Changed the option from Filter based on genomic location to Filter based on annotation in filter menu
    • Made the gene section naming more intuitive in classify regions by gene section report
    Bug Fixes:
    • Fixed a bug on .vcf importer
    • Fixed bugs on Mac OS X 10.10

    • Support for Affymetrix Mouse transcriptome Assay 1.0 (MTA) array
    • Added probe intensity information of Illumina Infinium HumanMethylation450 array to allow copy number analysis
    • Added interactive visualization function hierarchicacl clustering between the spreadsheet and viewer on selection
    • Added function to export gene list from multiple selected pathways in pathway enrichment result spreasheet
    Bug Fixes:
    • Fixed a bug of software crash caused by numeric overflow
    • Other Minor bug fixes

    • Improved the viewer on Mac Retina display
    • Improved the way handling miRNA-mRNA integration when there is no gene symbol annotation for some of the probesets
    • Changed the default setting on minimum number of reads to report unexplained regions in RNA-seq quantification dialog
    • Changed the default setting on hierarchical clustering to no show degrogram scale
    • Other Minor bug fixes

    • Support for 64-bit Mac OS X Mavericks
    • Fixed a bug on hierarchical clustering on a single item
    • Fixed a bug on genomic transpose function

    • Improved the PCA (from tools menu) correlation matrix on handling some variables contains only missing values
    • Improved the quantification in RNA-seq when using bam file as annotation
    • Fixed a bug on miRNA-seq quantification dialog error
    • Fixed a bug on importing Flow aligned data node project
    • Fixed a bug on create gene list from GO enrichment result

    • Miscellaneous minor bugs fixes

    • Improved color by cluster option in hierarchical cluster viewer
    • Fixed a bug in GO ANOVA step

    • Make human genome build default as hg19 instead of hg19_canonicalTranscripts
    • Make the chip name drop-down box expandable in the file properties dialog
    • Fixed a bug on finding region overlaps
    • fixed a bug on handling genomic properties when changing the species information on file properties dialog.

    • Improved the speed of quantification analysis in RNA-seq workflow
    • Added report on coefficient for diagonal discriminant model
    • Minor bug fixes

    • Fixed a bug on PCA when draw ellipsoid
    • Fixed a bug on scaling the data to mean, median etc. descriptive stats

    • Add SWAN normalization option on .idat importer for Illumina 450K methylation array
    • Add report on posterior probability on SVM prediction model
    • Improve the speed on bam file importer
    • Specify species information during Affymetrix HTA array import
    • Change p-value from ? to 1 of ANOVA result if a factor of two groups having the same values
    • Fix a bug on LOH creation
    • Other minor bug fixes

    • Add coefficients output for lda and pls for model selection
    • Add posterior probability to logistic regression test report
    • Add support to Affymetrix CelGene array
    • Changed the order of samples on chrview6.4 to have first sample left most
    • Improved on HTA2 array import handling mps files, disabled extended and full options
    • Improved on Illumina 450K idat Methylation array import only show file name instead of whole path
    • Fixed a bug in Illumina 450K Methylation array annotation

    • Add .idat importer for Illumina 450K Methylation array
    • Fixed a bug on pathway enrichment
    • Fixed a bug on SVM regression mean square error report

    • Added QC metrix RLE and AUC on Affymetrix HTA2.0 cel file import
    • Improved on File>Merge Files function, allow to merge genotyping call files
    • Improved accuracy on gene selection in Partek Pathway

    • Support Affymetrix HTA2.0 chip
    • Support vcf/bcf file import
    • Fixed a bug on quantification in PGS not use user specified temp directory

    • Speed up the importer on exon/gene array cel file import

    • Added Fluidigm importer
    • Fixed a reading .ppj file bug
    • Fixed an exon array importer with no summarization bug

    • Fixed a bug of RNA-seq quantification summary report on intronic reads percentage

    • Improvement on bcf/vcf importer
    • Minor bug fixes

    • Gene level data on Affymetrix Gene array, the file properties annotation is showing transcript annotation instead of probeset annotation
    • Added exon reads and RPKM spreadsheets during RNA-seq quantification
    • Added alt-splicing detection at exon level in RNA-seq workflow
    • Change wording on classify gene section result to be more specific on gene section
    • Make the sample in alphabetic order for heat map and segmentation region tracks in chromosome view, so they are consistent
    • Improved the default chrview on NGS data heatmap, show sample names on the left
    • Importing bam files not re-sort the file if it is sorted
    • Change wording from “Browse to row” to “Browse to location"

    • Add back 6.5 Hierarchical clustering viewer
    • Better handling on invoking IPA without valid spreadsheets open

    • Add QC metrics option on miRNA expression workflow for Affymetrix platform

    • Add support to Affy Gene-1_1-st array
    • Add genome and transcriptome library files automatic download for rn5 and mm10

    • Add support on Affymetrix Axiom chip for copy number and LOH analysis
    • Add support on nanoString version 1.7
    • Add support on ImaGene new format import
    • Add miRNA quantification database for mm9 and rn4

    • Add support on Affymetrix new miRNA chip library format
    • Add automatic library file download for Affymetrix BovGene-1.0 and ZeGene-1.0 arrays
    • Add support on Affymetrix CytoScanHD array for copy number analysis


    • Improvement on .bam/.sam import
    • Improvement of RNA-seq quantification
    • Add import for Partek Flow zipped project
    • Add methylation workflow
    • Add miRNA seq workflow
    • Add option to allow annotation creation from bam
    • Add quality information on SNP detection result
    • Add more annotation option on SNP result
    • Add raw reads information on RNA-seq (miRNA-seq) quantification

    • Improvement on allele ratio algorithm in unpaired copy number analysis
    • Added Illumina Text Genotyping/CNV Final Report importer
    • Add NanoString gene expression importer
    • Add detect LOH from allele ratio
    • New visualization improvement
    • Chromosome view
    • Hierarchical clustering viewer
    • SOM viewer
    • Profile Trellis
    • Improvement on result spreadsheet of finding overrepresented miRNA in miRNA workflow
    • Add Partek pathway integration
    • Add Taqman assay search in batch search¿assay awareness program
    • Add new normalization methods
    • Add new features model selection


Frequently Asked Licensing Questions

Version Questions


License Questions


Installation Questions

Using a Mac & Connecting to a Server

Get the disk image (.dmg file) from the Software Downloads tab. After downloading, double-click it. After the disk image mounts, just drag and drop the red Genomics Suite icon into your Applications folder. Then unmount the disk image by pressing the round eject button from the Finder.

The easiest way to connect to a license server from a Mac is to place a copy of the license server's license.dat file in the Macintosh HD > Users > Shared folder. This method will not work for Partek versions earlier than 6.5. You may have to contact the license administrator to get a copy. Then open the file (any text editor should do) and delete everything but the first line (the SERVER line). Then add this as the second line:


There's a reference to this method of connection on page 17 of the "Reading a License File" chapter of the FLEXnet License Administration Guide.

If for some reason you don't have access to the license file, then following is another method of connecting, which involves more work. You need to set up a .flexlmrc file in your HOME (that is, the folder that appears with a house icon in the Finder) that contains the string:


If your license server/license file is not configured to use ports due to a firewall, then you can skip the port. If you're not sure about the license server's name or ports, then check with your license administrator.

For example:

Here are instructions for doing this with TextEdit:

Open Finder → Applications → TextEdit, change the format to plain text (Format → Make Plain Text), and enter in the above string followed by the "Enter" key (this final keystroke is important). Next, use the File → Save As dialog to save the file as .flexlmrc in your HOME. Use a default text encoding of Unicode (UTF-8), and make sure the box "If no extension is provided, use ".txt"" is unchecked. When asked about using files that start with a dot, choose "Use "."".

If you have any problems, please send an email to our Licensing team.

Version Questions

  • Q: How do I know what version of Partek I am running?
    • A: To find out the version of Partek you are currently running, go to the Help menu within Partek and select About Partek Genomics Suite. The About Genomics Suite dialog will display the version of the software, along with the build number, which reflects the date that the installation executable was created. The version is located in the upper right corner and is in a x.xx.xxxx format.

  • Q: How do I read the version number?
    • A: The version number is in the following format 6.08.xxyy, with "xx" referring to month, and "yy" refering to day. For instance, version 6.08.0812 was released on August 12, 2008, but is older than version 6.08.0903, which was released on September 3, 2008.

License Questions

  • Q: What is the difference between a node-locked and floating license?
    • A: Node-locked licenses are locked to a specific machine to ensure software access. The node-locked license allows the benefit of always having a license available. Floating licenses can alternatively be configured to float across a network, independent of the operating platform and can run on multiple platforms at the same time. The benefit of the floating license is that Partek can be installed on many machines, while only requiring enough licenses to satisfy the maximum number of concurrent users.

  • Q: What platforms does Partek run on?
    • A: Partek currently runs on Windows 2000/XP/Vista/7 (32-bit and 64-bit), Intel-based Mac OS X Leopard, Snow Leopard, and Lion (32-bit only), and Linux (32-bit and 64-bit).

  • Q: Will Partek run on my PowerPC Mac?
    • A: Partek currently runs on Intel-based Macs, only.

  • Q: I have Linux, what kind of license configuration is available to me?
    • A: A floating license configuration is available for Linux. Node-locked licenses are not available for Linux.

  • Q: Does Partek allow for remote-access?
    • A: Floating licenses, hosted on a non-virtual license server, handle the cases of remote client access, whether they are dedicated user machines (running one instance of Partek) or large servers (capable of running multiple instances of Partek). Node locked licenses on any machine do not work for remote users.

  • Q: I am a License Administrator, how can I find out how many licenses are being used? / I just received a "Licensed Number of Users Already Reached" message. What does that mean?
    • A: You can find out who is using a license at any time from the "Server Status" tab of lmtools.exe. This tool should be in the FLEXnet folder on the license server. We also distribute a copy with the Genomics Suite - in the "C:\Program Files\Partek Genomics Suite\bin" folder of any client. The license administrator can also monitor usage by manually inspecting the license server's log file. It's usually named "log.txt" and in the FLEXnet folder. The file is straightforward enough so that the administrator should be able to get a good summary of overall license usage by looking at its contents. There is a way to get the license server to generate reporting information, but this information is dumped out in a proprietary format that can only be read by FLEXnet Manager - third party software from Acresso, the vendors of our FLEXnet Publisher licensing software.

Installation Questions

  • Q: I have a node-locked license. Do I need to grant other users on the machine that houses the license administrative privileges to be able to access Partek?
    • A: After the Admin User installs the Partek software, anyone with an account on and physical access to that machine, has access to the software, so admin privileges for each user is not necessary.

  • Q: I have retired the machine that housed Partek. Can I transfer my license to another machine?

Updates to the library and database files can be found on Library Files Updates page.