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Geneious 7.1

Software platform for the organization and analysis of biological data.

 

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Geneious 7.1 facilities

Vendor
Vendor`s Webhttp://www.biomatters.com
Biomatters Ltd webshot
OSWindows 2000, Windows XP, Windows Vista, Windows 7, Mac OS, Linux, 64-bit (x86_64)
Limitationsnot specified
Actualizedmore than year ago
Downloads2348
LocalizedEnglish
LicenseFree to try
SnapshotGeneious snapshot
Snapshot of Geneious

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Geneious manufacturer description

Geneious 7.1 Pro™ is an integrated and extendable software platform for the organization and analysis of biological data that runs on all major operating systems. Geneious Science Pro is a revolutionary bioinformatic tool that combines industry-leading DNA and protein analysis tools into a single package that is both ultra-powerful and easy to use. Scientists, researchers and students are able to search, organize and analyze genomic and protein information of any size via a single powerful desktop program that provides publication-ready images to enhance the impact of your research.
NGS Assembly

  • Assemble 454, SOLiD™ and Illumina™

  • Reference and de novo assembly

  • Hybrid (mixed data) assembly

  • Paired-end and mate pair assembly

  • Velvet, Maq, Bowtie on Geneious Server™


Alignment

  • ClustalW (Greenbutton™ enabled)

  • MUSCLE and MAFFT alignment

  • Kalign plugin (coming soon)

  • Translation and profile alignment

  • MAUVE genome alignment


Chromatogram Assembly

  • Chromatogram assembly of Sanger data

  • Import Sequencher data from .CAF file

  • Assemble by name

  • Call secondary peaks

  • Phase variation and heterozygous INDELs 


Phylogenetics

  • MrBayes (Greenbutton™ enabled)

  • PAUP* interface including ModelTest

  • NJ, UPGMA and PhyML

  • Bootstrapping and consensus trees

  • Interactive tree viewing

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Free download Geneious 7.1

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Geneious categories

phylogenetic, sequence, assembly, alignment, bioinformatics, BLAST, structure, cloning, NCBI, protein, primer

What is new in 7.1 changeinfo log

  • De novo assembly: Added option to produce circular contigs when the ends match
  • De novo assembly: Better results on data with gappy error models (e.g. IonTorrent or 454 data)
  • De novo assembly: Reduced size and improved performance on large lists of consensus sequences produced
  • Strip Alignment Columns: Add an option to remove columns that contain at least one ambiguity
  • Strip Alignment Columns: Add an option to strip two columns per codon
  • Extract Annotations: Added options to include upstream, downstream and intergenic regions of matching annotations
  • Compare Annotations: Easier to use interface, better results, more powerful options (including 3 way comparison), and results include annotation properties
  • Statistics: Added molecular weight of short nucleotide sequences
  • Primers can now be ordered from Eurofins MWG Operon via link on the Text View of oligo sequences
  • Alignment Viewer: Added option to number bases in the consensus sequence
  • Sequence Viewer: Improved performance when scrolling with the mouse wheel
  • Sequence Viewer: Displays the name of the track which an annotation is in the popup text when hovering over an annotation
  • Shared Database: Added the ability to set the group for new folders to be inherited from the parent folder in addition to the user's primary group
  • SAM/BAM importer: Improved performance
  • Tutorials: Import into a sub-folder instead of putting all the files directly in the folder they are dragged into
  • Identify Organism Workflow: It also includes the taxonomy fields (where available) on each sequences identified
  • Distance matrix: Decimal places option is not available for similarity
  • Primer testing: now works on the consensus (in a similar way to designing) when run on alignments and contigs
  • General performance improvements
Bugs fixed:
  • Read Mapping: Better results in some cases and fixed rare crash when mapping to a circular reference sequence
  • Info Properties Viewer: Long values wrap to the next line instead of disappearing off the right hand side of the view
  • Alignment Viewer: Fixed crash when saving after changing the genetic code on non-editable alignments
  • Sequence Viewer: Fixed poor performance rendering translation when there are translation annotations with lots of short intervals
  • Sequence Viewer: Fixed crash sometimes when opening sequence with tracks on it in a new window
  • Sequence Viewer: Fixed consensus sequence being assigned quality differently than how the consensus operation assigned quality around homopolymer regions
  • Newick Export: Exports multiple bootstrap trees instead of just the first one
  • SAM/BAM Import: Fixed failure to import some files which have padded alignments
  • Assemble by name: Fixed excessive memory usage leading to out of memory error
  • NCBI Blast: Fixed crash when binning into has hit vs no hit when run on sequences in alignments
  • Read Mapping: Fixed tracks on input reads not appearing in output contig when mapping to all matching locations
  • MUSCLE alignment: Update MUSCLE to version 3.8.425 which fixes problems aligning a long sequence
  • Annotation editing: Fixed crash when editing annotations on 0 length sequences
  • Annotation filtering: Fixed not equals (!=) clause giving incorrect results
  • Internet connection: Switched Geneious to prefer ipv4 to fix internet connection issues encountered by people whose firewalls, virus scanners, or proxy servers don't support ipv6
  • Annotate From and Transfer Annotations: 'Translation' properties on the source annotations are removed and replaced with a 'Transferred Translation' property
  • Annotate From: Fixed documents becoming excessively large when iteratively transferring annotations by using newly annotated sequences as source sequences for future annotation
  • Consensus Alignment: Fixed crash if document is modified while alignment is in progress
  • Consensus Alignment: Fixed crash sometimes when run on mixture of alignments and stand-alone sequences
  • Variant Finder: If find variants is run when there were unsaved changes on a small contig with paired reads, variants near the ends of the contig were wrongly filtered out due to strand bias
  • Extracting sequences: If an identical annotation is present in multiple tracks, it would only appear in one of the tracks in the extracted sequence
  • Performance: Fixed occasional hangs and poor performance when local documents contains 100,000+ documents
  • Workflows: Fixed failure to compile custom code workflows after Geneious had crashed or locked up earlier.
  • Workflows: Fixed crash on some documents when using the 'Filter Documents' workflow step
  • VCF importer: Properly support missing data fields
  • Annotations Table: Fixed crash sometimes when selecting multiple contig documents
  • Extract Annotations: Fixed a bug where the option to only include contained annotations wasn't working correctly.
  • Fixed occasional crashes that can happen at any time while Geneious is checking if any new plugins are available.
  • Fixed occasional crashes when working with folders with hundreds of documents in them
  • Custom Blast: Fixed a bug where Custom BLAST databases could get into a corrupt state if deleted during blast operations.
  • Custom Blast: Fixed crash when working with Custom BLAST databases that contain invalid nucleotides in the fasta file
  • Network drives: Fixed crash and improved performance if data location is set to a network drive

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End user agreement for Geneious

Biomatters` Geneious Software License Agreement   By downloading, installing and/or running this Software, you are consenting to be bound by and are a party to this Agreement. This is a grant of License allowing the Licensee to use the software program Geneious (hereafter referred to as "Geneious" or the "Software") under certain restrictions, terms and conditions. As used herein, the term "Licensee" shall refer to the person or entity downloading, installing and/or using Geneious. "Authorized User" shall refer to the Licensee, if the Licensee is an individual person. If the Licensee is an academic institution, "Authorized User" shall refer to any student, faculty or staff member authorized by the Licensee to use the Software while performing duties within the scope of their employment or assignment. If the Licensee is a commercial organization, "Authorized User" shall refer to any employee, independent contractor or temporary worker authorized by the Licensee to use the Software while performing duties within the scope of their employment or assignment. "Licensor" shall refer to Biomatters Limited and/or any person or entity who has been duly and properly authorized by Biomatters Limited to act as a Licensor. <strong>License Grant:</strong> The Software is the property of the Licensor. The Software is licensed, not sold. Title and copyrights to the Software, in whole and in part and all copies thereof, and all modifications, enhancements, derivatives and other alterations of the Software regardless of who made any modifications, if any, are, and will remain, the sole and exclusive property of the Licensor. The Licensor grants to the Licensee a non-exclusive, non-transferable License to use the Software in the manner described in this document. Upon purchase or subscription of a License, the Licensee will receive a unique key-code (hereinafter referred to as a "License Key") that enables an Authorized User to use the Software according to the terms and conditions of the specific License type as described below. Only the Licensor is permitted to produce License Keys for the Software. <strong>Single User License:</strong> Upon purchase or subscription of a Single User License, the Licensee may install and use the Software on 3 computers running any of the supported operating systems, provided that the same License Key is not used by different Authorized Users on different computers. Academic and Student Single User Licenses allow the Licensee to use the Software for personal, academic and non-commercial purposes only. <strong>Concurrent License:</strong> Purchase or subscription of Concurrent Licenses permits the Licensee to install and use the Software on an unlimited number of computers running any of the supported operating systems on the same network, and for multiple Authorized Users to use the Software on different computers on that network concurrently, provided that the number of Authorized Users using the Software on different computers concurrently will be limited to the number of Concurrent Licenses registered to the Licensee and currently active. <strong>Duration and Termination of License Grant:</strong> Purchase of a License that is not a time limited subscription License allows the Licensee to use the Software for an unlimited period. A subscription License (including one month Licenses) is time limited and allows the Licensee to use the Software for the period subscribed. Supcription license are valid from date of issue. At the end of the subscription period the License granted under this Agreement will terminate, unless the subscription is renewed for a further period. Notwithstanding the above, this Agreement and the License granted hereunder will terminate automatically if Licensee fails to comply with the limitations described herein. Upon termination, Licensee must destroy all copies of the Software. <strong>Software Upgrades:</strong> Purchase of a License that is not a time limited subscription License entitles the Licensee to free upgrades of the Software for one year following date of purchase. A subscription License (including one month Licenses) entitles the Licensee to free upgrades of the Software during the period subscribed. <strong>Support:</strong> Purchase of a License that is not a time limited subscription License entitles the Licensee to free technical support from Biomatters Limited via email for one year following date of purchase. A subscription License (including one month Licenses) entitles the Licensee to free technical support from Biomatters Limited via email for the duration of the subscription. <strong>Other Terms Applicable to License Grant:</strong> Licensee may copy the Software for archival purposes, provided any copy must contain all of the original Software`s proprietary notices. Licensee may not:
<li>Modify, translate, reverse engineer, decompile, disassemble (except and SOLELY to the extent that an applicable Statute expressly and specifically prohibits such restrictions), or create derivative works based on the Software;</li>
<li>Copy the Software other than as specified above;</li>
<li>Rent, lease, grant a security interest in or otherwise transfer rights to the Software;</li>
<li>Remove any proprietary notices or labels on the Software.</li>
  <strong>Disclaimer of Warranty:</strong> The version of the Software is provided on an AS IS basis, without warranty of any kind, including, without limitation, the warranties that the Software is merchantable, fit for a particular purpose or non-infringing. The entire risk as to the quality and performance of the Software is borne by you, the Licensee. Should the Software prove defective in any respect, Licensee and not Biomatters Limited, nor any of its Distributors or Resellers, shall assume the entire cost of any service and repair required. In addition, the security mechanisms implemented by the Software have inherent limitations and Licensee must determine that the Software sufficiently meets Licensee`s requirements. This Disclaimer of Warranty constitutes an essential part of the License Agreement. No use of the Software is authorized hereunder except under this Disclaimer. <strong>Title:</strong> Title, ownership rights and intellectual property rights in the Software shall remain with Biomatters Limited. The Software is protected by copyright and other intellectual property laws and by international treaties. Title and related rights in the content accessed through the Software is the property of the applicable content owner and is protected by applicable law. The License granted under this Agreement gives the Licensee no rights to such content. <strong>Termination:</strong> This Agreement and the License granted hereunder will terminate automatically if Licensee fails to comply with the limitations described herein. Upon termination, Licensee must destroy all copies of the Software. <strong>LIMITATION OF LIABILITY:</strong> UNDER NO CIRCUMSTANCES AND UNDER NO LEGAL THEORY, TORT, CONTRACT OR OTHERWISE, SHALL LICENSOR OR ITS SUPPLIERS OR RESELLERS BE LIABLE TO LICENSEE OR ANY OTHER PERSON FOR ANY INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY CHARACTER INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, PROFIT, WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION OR ANY AND ALL OTHER COMMERCIAL DAMAGE OR LOSSES. IN NO EVENT WILL LICENSOR BE LIABLE FOR ANY DAMAGES IN EXCESS OF THE AMOUNT LICENSOR RECEIVED FROM LICENSEE FOR A LICENSE OF THE SOFTWARE, EVEN IF THE LICENSOR SHALL HAVE BEEN INFORMED OF THE POSSIBILITY OF SUCH DAMAGES, OR FOR ANY CLAIM BY ANY THIRD PARTY. THIS LIMITATATION OF LIABILITY SHALL NOT APPLY TO LIABILITY FOR DEATH OR PERSONAL INJURY RESULTING FROM THE LICENSOR`S NEGLIGENCE TO THE EXTENT APPLICABLE LAW PROHIBITS SUCH LIMITATION. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OR LIMITATION OF INCIDENTAL OR CONSEQUENTIAL DAMAGES, SO THIS EXCLUSION AND LIMITATION MAY NOT APPLY. <strong>Export Law Assurances:</strong> Licensee agrees and certifies that neither the Software nor other technical data received from the Licensor, nor the direct product thereof, will be exported out of the United States except as authorized and permitted by the laws and regulations of the United States. If the Software has been rightfully obtained by Licensee outside of the United States, Licensee agrees that Licensee will not re-export the Software nor any other technical data received from the Licensor nor the direct product thereof, except as permitted by the laws and regulations of the United States and the laws and regulations of the jurisdiction in which Licensee obtained the Software. <strong>High Risk Activities:</strong> The Software is not fault-tolerant and is not designed, manufactured or intended for use or resale as on-line control equipment in hazardous environments requiring fail-safe performance, such as in the operation of nuclear facilities, aircraft navigation or communication systems, air traffic control, direct life support machines or weapon systems in which the failure of the Software could lead directly to death, personal injury or severe physical or environmental damage ("High Risk Activities"). Accordingly, Licensor and its suppliers specifically disclaim any express or implied warranties of fitness for High Risk Activities. <strong>Miscellaneous:</strong> This Agreement represents the complete agreement concerning the License granted hereunder and may be amended only by a writing executed by both parties. <strong>Section 508 of the Rehabilitation Act for Electronic and Information Technology Accessibility for Persons with Disabilities</strong> The Geneious software has not been designed to conflict with any compliance areas of section 508 of the Rehabilitation Act for Electronic and Information Technology Accessibility for Persons with Disabilities. We endeavour to make all future development of the Software fully compliant with all areas of Section 508. Primer3 Copyright Notice and Disclaimer Copyright (c) 1996,1997,1998,1999,2000,2001,2004 Whitehead Institute for Biomedical Research. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
<li>Redistributions must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Redistributions of source code must also reproduce this information in the source code itself.</li>
<li>If the program is modified, redistributions must include a notice (in the same places as above) indicating that the redistributed program is not identical to the version distributed by Whitehead Institute.</li>
<li>All advertising materials mentioning features or use of this software must display the following acknowledgment: <em>This product includes software developed by the Whitehead Institute for Biomedical Research.</em> </li>
<li>The name of the Whitehead Institute may not be used to endorse or promote products derived from this software without specific prior written permission.</li>
We also request that use of this software be cited in publications as Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) <em>Bioinformatics Methods and Protocols: Methods in Molecular Biology.</em> Humana Press, Totowa, NJ, pp 365-386<br />Source code available at http://fokker.wi.mit.edu/primer3/. THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS`` AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.