Fedora 20 Update: ugene-1.14.0-1.fc20

[updates at fedoraproject.org]

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Fedora Update Notification
FEDORA-2014-9258
2014-08-08 07:46:10
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Name        : ugene
Product     : Fedora 20
Version     : 1.14.0
Release     : 1.fc20
URL         : http://ugene.unipro.ru
Summary     : Integrated bioinformatics toolkit
Description :
Unipro UGENE is a cross-platform visual environment for DNA and protein
sequence analysis. UGENE integrates the most important bioinformatics
computational algorithms and provides an easy-to-use GUI for performing
complex analysis of the genomic data. One of the main features of UGENE
is a designer for custom bioinformatics workflows.

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Update Information:

Important changes in this major release include:

Help system:

Help buttons were added into all UGENE dialogs.
The documentation was moved to the Atlassian Confluence system, this makes it easier to search for required information in it.
Shared storage: sharing of bioinformatics data in a lab. For details, see this page.

Alignment Editor:

Overview for a multiple alignment was added, a lot of configuration options are available.
A multiple alignment consensus can now be exported.

Phylogenetic Trees:

PhyML Maximum Likelihood was integrated.
It is now possible to re-root a tree.
Circular View and circular sequences: a possibility to mark a nucleotide sequence as circular was added. This mark affects how a pattern is searched in the sequence – results located over the end-start junction of it are also found.
Plasmid features: auto-annotation of the plasmid features like promoters, regulatory regions, primers, etc.
Export images: exporting of images was improved (multiple alignments, circular molecules, etc.)

NGS:

BWA-MEM tool for aligning short reads was integrated. The tool is available in the GUI dialog and in the Workflow Designer.
Different workflow elements for sorting, merging and filtering and trimming of NGS data were added (BAM and FASTQ files).
UGENE Public Storage: the storage can be remotely accessed from any UGENE instance. It contains common genomes and hundreds of plasmids.
A splash screen was added on the UGENE startup.

http://ugene.unipro.ru/news.html#010814
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ChangeLog:

* Mon Aug  4 2014 Yulia Algaer <yalgaer at unipro.ru> 1.14.0-1
- Upstream version change
* Tue Jun  3 2014 Yulia Algaer <yalgaer at unipro.ru> 1.13.3-1
- Upstream version change
* Tue Apr 15 2014 Yulia Algaer <yalgaer at unipro.ru> 1.13.2-1
- Upstream version change
* Thu Feb 20 2014 Yulia Algaer <yalgaer at unipro.ru> 1.13.1-1
- Upstream version change
* Wed Dec 11 2013 Yulia Algaer <yalgaer at unipro.ru> 1.13.0-1
- Upstream version change
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This update can be installed with the "yum" update program.  Use
su -c 'yum update ugene' at the command line.
For more information, refer to "Managing Software with yum",
available at http://docs.fedoraproject.org/yum/.

All packages are signed with the Fedora Project GPG key.  More details on the
GPG keys used by the Fedora Project can be found at
https://fedoraproject.org/keys
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