Work with various scientific and research data on your computer. Collect, organize, analyze, and search genomic and protein information. View images of bacterial genomes or human chromosomes and use pipelines and a wide range of tools to perform complex analyses.
Geneious is a research tool designed for biologists and not computer scientists.
Main features:
- Drag and drop to convert and import sequence data.
- Powerful SNP detection and variant calling.
- Streamlined microsatellite genotyping.
- Tree building and viewing without juggling files.
- Add your favourite algorithm, database or visualization to Geneious.
v7.1 [Mar 19, 2014]
New Core Features
Molecular Cloning
Gibson Assembly - One-step cloning of fragments using Gibson assembly including automated primer design and batch cloning/shuffling
Codon Optimization - Find rare codons or produce a fully optimized sequence based on a target organism and remove unwanted restriction sites at the same time.
TOPO Cloning - One-step cloning of fragments into a vector using TOPO
Searchable, selectable and sortable enzyme table. Now has a search box to find enzymes by name
Primer Design
Dynamic Primer Design
Primers are now designed on the consensus of alignments and contigs
Redesigned Add 5' extension operation that allows adding several extension parts in one step
New in the R7 Update
Primers can now be ordered from Eurofins MWG Operon via link on the Text View of oligo sequences.
Alignment, Assembly and Mapping
Added visualization of minimum/mean/maximum coverage when zoomed out.
Added highlight coverage above threshold option.
Consensus: When coverage or quality is below a specified threshold you can choose to call either ?, N, Gap, or the reference sequence value.
New in the R7 Update
All newly created contigs will have a mean coverage field in the document table.
All newly created reference sequence contigs will have a '% of reference sequence covered' field
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
Annotation, Analysis and Prediction
Copy and Paste Annotations - Annotations are now maintained when copying sequences! Highlight part of a sequence, copy with ctrl c and then paste it using ctrl v into another location and the annotations will be preserved.
Exporting Graphs
New in the R7 upgrade
Compare Annotations: Easier to use interface, better results, more powerful options (including 3 way comparison), and results include annotation properties
Extract Annotations: Added options to include upstream, downstream and intergenic regions of matching annotations
Statistics: Added molecular weight of short nucleotide sequences
New Plugins
Tree Building and Viewing
RAxML - Randomized Axelerated Maximum Likelihood
GARLI - Genetic Algorithm for Rapid Likelihood Inference
FastTree - Approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences
Alignment, Assembly and Mapping
LastZ - BLAST-like alignment tool for the pairwise alignment of chromosome-sized nucleotide sequences
Bowtie2 - Short read aligner
Assembly
Velvet - De-novo assembler for very short reads
New in the R7 Update
TopHat- Fast splice junction mapper for RNA-Seq reads.
MIRA-Specialised assembler for sequences with a high number of repeats
