Win7 Download
bookmark Windows 7 Download add as favorite Windows 7 Download Windows 7 Download RSS register at Windows 7 Download

Staden for Windows 7 - Fully developed set of DNA sequence assembly - Windows 7 Download

Staden Windows 7

Staden 2.0.0b9

A fully developed set of DNA sequence assembly (Gap4 and Gap5)

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

Staden 2.0.0b9 full details

File Size: 20.00 MB
License: Open Source
Price: FREE
Released: 2011-12-05
Downloads: Total: 511 | This Month: 0
Publisher: Rodger Staden
Publisher URL: http://staden.sourceforge.net/


Download Staden 2.0.0b9

Save Staden to My Stuff

View full Staden 2.0.0b9 screenshot
Staden

User Rating: 3.2 (13 votes)

Staden - Windows 7 Download awards

Staden windows 7 compatible windows 7 download editor's pick

Staden 2.0.0b9 full description

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

Staden Package 2.0.0b8:

The latest release of the main Staden Package (comprising gap4, gap5, spin, trev and ancillary tools) has just been uploaded.

This is the first release since 1.7 to run on Microsoft Windows again (tested on Vista and XP) and we've also added imroved support for MacOS X thanks to the wonderful open-source community. In addition to that most of the documentation is complete for Gap5. These factors combined means that 2.0 is close to non-beta at long last - probably the next release.

The source is already available. I'll be uploading precompiled binary distributions for various platforms over the remainder of the week, so if they're not available yet, please check in a few days.

Gap5/tg_index 1.2.11

General changes

* Microsoft Windows version. The code should now compile and run under MinGW/Msys on windows.

* MacOS X updates: improved compilation and fixed a few Mac specific display glitches.

* Various code tidyups - less compiler warnings, more portable for linux variants (eg Centos).

* Removed dependency on samtools. (This also avoids a few samtools related bugs, but hopefully not creating new ones to
replace them.)

* Removed dependency on IncrTcl, IncrTk, IncrWidgets. These can still be used for one part of Gap4 (prefinish GUI) but the
code will build and execute without these now.

Gap5 changes

* In-program help should now be working.

* A Disassemble Readings option has been added to the main Edit menu. (This performs the same task as in Gap4.)

* Tg_index now supports the CAF, fasta and fastq formats. When importing fasta/fastq we just create single-read contigs, so it's simply an easy way of importing consensus sequences or a *few* finishing reads. CAF support will import entire assemblies though. Also improved the CAF exporting code.

* First draft of a Find Read Pairs function (as in Gap4). At present read-pair orientation needs some work still, but the
basic plot and searching is working.

* Internal record numbers are now 64-bit instead of 32-bit, removing the need for reserving sequence record IDs in tg_index (-r option) and allowing for more than 2 billion sequences in a gap5 db.

* Contig editor "tag macros" (from gap4) have been added. Use Shift + function key to define a tag macro and then that
function key to apply it.

* A "readings" list now exists (as in Gap4) which is displayed and can be populated using the contig editor "names" panel. The copying (cut/paste) of read names binding has also changed from left-click+drag to middle-click, now matching Gap4.

* Quality value 100 now has a special meaning for the consensus algorithm, as in Gap4. It forces the base to be considered as
true (as it's only possible via a manual edit).

* More contig editor key bindings: Page up/down (already existed for scrolling in 1Kb) can be modified by Shift, Control or Shift+Control to scroll in 10, 100 and 1000Kb steps; [,] keys for setting base quality to 0 or 100; Shift Up/Down arrow and
Control Up/Down arrow for incrementing/decrementing base qualities by 1 or 10.

* Editor Delete now only works on pad characters unless Control Delete is used, in order to prevent accidental removal of real
data.

* Added contig editor "Save Settings" command.

* Internal changes to the template display and Tk canvas.

* Sped up contig editor when dealing with excessively deep alignments.

* Reading names in the contig editor are now be selected for copy and pasting using the left mouse button.

* Tg_index now has a -q option to limit the number of unpaired reads held in memory (for the "-p" option). This significantly
reduces the memory usage on large data sets, at the expense of longer running times.

Staden 2.0.0b9 download tags

Windows 7 free download

Bookmark Staden

copy windows 7 bookmark
copy windows 7 bookmark
copy windows 7 bookmark

Staden for Windows 7 - Copyright information

All Staden reviews, submitted ratings and written comments become the sole property of Windows 7 download. You acknowledge that you, not windows7download, are responsible for the contents of your submission. However, windows7download reserves the right to remove or refuse to post any submission for any reason.

Windows 7 Download periodically updates pricing and software information of Staden full version from the publisher, but some information may be out-of-date. You should confirm all information.
Using warez version, crack, warez passwords, patches, serial numbers, registration codes, key generator, pirate key, keymaker or keygen for Staden license key is illegal and prevent future development of Staden. Download links are directly from our mirrors or publisher's website, Staden torrent or shared files from free file sharing and free upload services, including Rapidshare, MegaUpload, YouSendIt, SendSpace, DepositFiles, DivShare, HellShare, HotFile, FileServe or MediaFire, are not used.

Staden users' reviews

Staden 2.0.0b9 review by rongyan (Mar 24, 2016)
it's very useful for us

Post Staden review

Your Name:
Product Version:
Rating:
Review:
Security Code:

Windows 7 Staden related downloads

... UGENE is a free visual software solution for DNA and protein sequence analysis. UGENE provides customizable tools ...
... 64-bit is a free visual software solution for DNA and protein sequence analysis. UGENE provides customizable tools ...
... available on DNAssist include: The conversion of a DNA sequence between the circular and linear forms The ...
CodonCode Aligner is user-friendly software for DNA sequence assembly, alignment, contig editing, and mutation detection.
Zoom and spin your way around the globe while viewing earthquakes in 3D. Adjust and ...
My Account
Help
Windows 7 Software Coupons
My Saved Stuff
You have not saved any software.
Click "Save" next to each software.

Would you like to receive announcements of new versions of your software by email or by RSS reader? Register for FREE!
Windows 7 Downloads Picks
Popular Tags
Popular Windows 7 Software
© 2018 Windows7Download.com - All logos, trademarks, art and other creative works are and remain copyright and property of their respective owners. Microsoft Windows is a registered trademarks of Microsoft Corporation. Microsoft Corporation in no way endorses or is affiliated with windows7download.com.