Geneious

Application data
Created by	Biomatters Limited
Biological application domain(s)	Phylogenetics, Sequence analysis, De-novo assembly, Whole Genome Resequencing, Alignment, systems biology, Comparative Genomics, SNP discovery, InDel discovery, Transcription Factor Binding Site identification, Genomics, Population genetics, Homology, Integrated solution, Metagenomics, Motif, Read alignment, Structural variants, RNA-Seq
Principal bioinformatics method(s)	Alignment, Assembly, Assembly visualization, Assembly validation, Alignment viewer, Annotation, Alignment Analysis, multiple sequence alignment viewer, Motif analysis, genetic variation annotation, Basecaller, Genome browser, Sample Barcoding, Database, Paired End, Differentially expressed gene identification, Genome browser, Integrated solution, Mapping, neighbor-joining, Smith-Waterman, command line tool wrappers, Visualisation
Technology	Sanger, Illumina, ABI SOLiD, 454
Created at	Auckland, New Zealand
Maintained?	Yes
Input format(s)	over 50 common file formats, FASTA, FASTQ, GenBank, SAM, Illumina, ELAND, CSFASTA/CSQUAL (ABI SOLiD)
Output format(s)	over 40 file formats
Programming language(s)	Java Swing
Licence	Basic (free for academic use) and Pro (commercial with discounts for academics and students)
Operating system(s)	Windows, Mac OS X, Linux, Solaris

Summary: Search, organize and analyze genomic and protein information of any size via desktop program that provides publication ready images to enhance the impact of your research.

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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.

With an email-like interface for easy navigation and extremely intuitive usability, Geneious Pro provides an intelligent central platform for biologists using all the major industry-leading algorithms and applications in bioinformatic research. Complex data such as entire bacterial genomes or human chromosomes can be stored, visualized and analyzed using a single desktop application that unites pipelines and tools and ensures analyses are easily repeatable.

Features

Geneious comes in a Basic version that is free for academic use, and a commercial Pro version with added features. Geneious bundles various bioinformatics tools under one hood with an easy-to-use email-client-like interface. See the release notes for a full list of features.

• Fast de novo and reference assembly
• Sequence searching (NCBI, PFam, Uniprot, BLAST) and publication searching (PubMed, Entrez)
• Automated search agents and smart agents - smart agents can be trained to search for other related documents
• Sequence alignment and sequence viewing - BLAST, MUSCLE, translation alignment, ClustalW on Greenbutton super-computer
• Motif search and open reading frame prediction
• Genome and protein annotations
• Phylogenetic tree building UPGMA, Neighbour joining with bootstrapping and consensus trees, PAUP* and PhyML plugin
• Contig assembly and chromatogram editing
• in silico cloning and Gateway cloning - Restriction digest, insert and ligate into vector, add attB sites, PB reaction, LR reaction
• PCR Primer design - designing and testing, degenerate primers, mismatches and multiple primer searching, implementation of Primer3
• Protein structure viewer
• Collaborate and share data over the internet
• Teach bioinformatics - Create tutorials with direct links to material in Geneious
• Public API to develop free bioinformatics plugin by the community
• Sassafras K2 license server support
• Various standard bioinformatics applications such as ClustalW, MrBayes, EMBOSS, Mauve, MUSCLE and PAUP*

Innovations that set Geneious Pro apart

• Next Generation Full Genome Assembly - Geneious Pro can seamlessly assemble regular or paired-end genomic data generated by Sanger, 454, SOLiD® and Solexa® sequencing technologies.
• Superb Visualizations - Geneious Pro is the only bioinformatics application that provides users with visualizations that make work seem like leisure
• GRID Computing - Geneious Pro is the only commercial bioinformatics application that allows you to harness the power of grid computing for Mr. Bayes and ClustalW through its world-first Greenbutton® Technology.
• Smart Agents - A unique feature of Geneious Pro enables researchers to train smart agents to seek, retrieve and sort data specific to user requirements from private and public databases such as NCBI, BLAST, Pfam and UniProt. Researchers can spend their time analyzing relevant data, not sifting and sorting.
• Secure Collaboration - A world first in science software, researchers can work together within Geneious Pro, share files and information on a project, and chat securely. This unique feature enables Geneious Pro researchers to collaborate worldwide on critical areas of discovery.
• Education Tutorials - Teach or learn bioinformatics interactively. Students are guided through analysis and exercises with all the data and tools just a click away. Geneious Pro also allows teachers to create their own tutorials using live links to data, and communicate with students using the built-in collaboration features.
• Plugin Architecture - The public API allows any developer to leverage the power of the Geneious Pro framework and extend it to any customized function.

Links

• Geneious Homepage [ edit link ]
• Geneious [ edit link ]

• Add a Link

References

1. . 2012. Bioinformatics (Oxford)

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