Plugin Community

Extend the functionality of Geneious with plugins written by us and the community

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Write your own plugins : The Geneious Plugin Development Kit (PDK) allows anyone to start extending Geneious with their own functionality

Phylogenetics

Phylogenetic inference using PAUP* 4.0
Bayesian phylogenetic analysis using MrBayes
Fast maximum-likelihood tree building on large datasets with RAxML
Assess putative species in phylogenetic trees
Phylogenetic inference for molecular evolution using PhyML
Fast phylogenetic tree building of huge datasets
Fast maximum likelihood tree building on large datasets with GARLI

Nucleotide Analysis

Search genomes for tandem repeats / microsatellites using Phobos
Identify heterozygotes in chromatograms with secondary peak calling
Predict genes in microbial DNA with Glimmer
Identify recombination events in phylogenetic history with DualBrothers
Find targets for DNA methylation by predicting CpG islands
Streamlined microsatellite genotyping
Complement or Reverse DNA sequences without doing both
Eukaryotic gene prediction with Augustus
CRT
Find existing CRISPR sites in bacteria and archaea
Automatically mutate or shuffle sequences
Predict transcription factors and protein coding regions
Haplotype based variant finding with FreeBayes.
Find polymorphic tandem repeats in alignments using Phobos
Find large, distant repeats

Protein Analysis

Services and Searching

Simplified submission of sequences, genomes, features, primers and traces.
Integrated chat client
Jump to documents by entering their unique IDs
Integrated laboratory information management system for DNA barcoding
Opens a terminal window inside Geneious for scripting in the Groovy language
List the size of all folders in your local database
Taxonomically classify samples against your own database of known sequences
All in one functional annotation tool and annotation data analysis
Search and download eukaryotic pathogen genes

Alignment

Align large genomes using LASTZ
Align multiple genomes to identify large-scale evolutionary events using Mauve
Fast and accurate multiple sequence alignment with MAFFT
Partition allele multisets from multiple alignments
Multiple sequence alignment using the latest addition to the Clustal family.

Assembly