Geneious
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 | |
| Developer(s) | Biomatters Ltd. |
|---|---|
| Stable release | R7 / 8 October 2013 |
| Operating system | Windows, Linux, Mac OS X |
| Platform | Java |
| Type | Bioinformatics |
| License | Personal, Floating |
| Website | www.geneious.com |
Geneious is suite of cross-platform bioinformatics software applications developed by Biomatters Ltd. The current version is Geneious R7, released in October 2013.
Features
Geneious bundles various bioinformatics tools with an email client-like interface. Features include:
- Fast de novo and reference assembly of illumina, SOLiD, 454 and Sanger data
- Paired-end visualization
- Split viewer for genome browsing, easy restriction analysis and cloning workflows
- Virtual gel viewer
- Microsatellite viewer
- Sequence searching (NCBI, 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, MAFFT, translation alignment, ClustalW MAUVE Genome Alignment
- Motif search and open reading frame prediction
- Genome and protein annotations
- Phylogenetic tree building UPGMA, Neighbour joining with bootstrapping and consensus trees, PAUP*, MrBayes 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. Gibson Assembly and Topo Cloning are included in Geneious R7.
- 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
- Sassafras K2 license server support
- Various standard bioinformatics applications such as ClustalW, MrBayes, EMBOSS, Mauve, MUSCLE and PAUP*
Geneious Plugins
Along with a core suite of bioinformatics tools, Geneious provides free plugins to extend functionality. These plugins may be created by anyone in the community using a Public API, providing the opportunity to wrap a popular algorithm in a biologist-friendly user interface.[1]
Phylogenetics
- PAUP* - Phylogenetic inference using PAUP*
- MrBayes - Bayesian phylogenetic analysis using MrBayes
- RAxML - Fast maximum-likelihood tree building on large datasets with RAxML
- Species Delimitation - Investigate diversity and new species from phylogenetic trees
- PhyML - Phylogenetic inference for molecular evolution using PhyML
- FastTree - Fast phylogenetic tree building of huge datasets using FastTree
- GARLI - Fast maximum likelihood tree building on large datasets with GARLI
Nucleotide Analysis
- Phobos - Search complete genomes for tandem repeats using Phobos
- Heterozygotes - Identify heterozygotes in sequences with secondary peak calling
- Glimmer Gene Prediction - Find genes in microbial DNA with Glimmer
- DualBrothers Recombination Detection -Identify recombination events in a phylogenetic history with DualBrothers
- CpG Islands - Find targets for DNA methylation by predicting CpG islands
- Microsatellite - Streamlined microsatellite genotyping
Protein Analysis
- Transmembrane Prediction - Predict transmembrane spanning regions of proteins
- PDB Structure Aligner - Structural alignment of PDB protein sequences
- InterPro Scan - Scan protein sequences against the InterPro database consortium
- Coiled Coils - Predict protein coiled coil regions
Services and Searching
- QuRe - Reconstruct viral quasispecies from next-generation sequencing data
- PlasmoDB and PiroplasmaDB - Search and download gene and protein information on eukaryotic pathogens
- GenBank Submission - Simplify the process of submitting sequences, genomes, features, primers and traces
- Collaboration - Integrated chat client
Alignment
- * LASTZ - Align large genomes using LASTZ
- * Mauve - Align multiple genomes to determine conserved genomic DNA with Mauve
- * MAFFT - Fast and accurate multiple sequence alignment with MAFFT
Assembly
References
External links
- Official website
- Biomatters website
- List of phylogeny software, hosted at the University of Washington
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