Geneious Prime Plugins

Extend the functionality and features of Geneious Prime with plugins for assembly, alignment, phylogenetics and more.

Alignment and Assembly

Multiple sequence alignment using the latest addition to the Clustal family

Align large genomes using LASTZ

Fast and accurate multiple sequence alignment with MAFFT

Align multiple genomes to identify large-scale evolutionary events using Mauve

Partition allele multisets from multiple alignments

Adapter/quality trimming and filtering

Fast and sensitive aligner for RNA and DNA

Reference mapping with Bowtie

Perform contig assembly using CAP3

A de novo assembler for single molecule sequencing reads, such as PacBio and Oxford Nanopore

A versatile mapper / pairwise aligner for genomic and spliced nucleotide sequences

Efficient and accurate sequence assembly with MIRA

De novo assembly of short reads with Velvet

Phylogenetics

Fast maximum-likelihood tree building on large datasets with RAxML

Fast phylogenetic tree building of huge datasets

Bayesian phylogenetic analysis using MrBayes

Phylogenetic inference using PAUP* 4.0

Phylogenetic inference for molecular evolution using PhyML

Species Delimitation

Assess putative species in phylogenetic trees

Sequence Analysis

Eukaryotic gene prediction with Augustus

Complement/Reverse

Complement or Reverse DNA sequences without doing both

Find targets for DNA methylation by predicting CpG islands

EMBOSS Mutate and Shuffle

Automatically mutate or shuffle sequences

EMBOSS Nucleotide Analysis

Predict transcription factors and protein coding regions

Haplotype based variant finding with FreeBayes.

Glimmer Gene Prediction

Predict genes in microbial DNA with Glimmer

Identify heterozygotes in chromatograms with secondary peak calling

Microsatellites

Streamlined microsatellite genotyping

Search genomes for tandem repeats / microsatellites using Phobos

Polymorphic SSRs

Find polymorphic tandem repeats in alignments using Phobos

Find large, distant repeats

Sequence Classifier

Taxonomically classify samples against your own database of known sequences

Protein Analysis

Predict protein coiled coil regions

EMBOSS Protein Analysis

Predict secondary structure, antigenic regions and signal cleavage sites.

Automatically annotate proteins with InterPro domains

PDB Structure Aligner

Structural alignment of PDB protein sequences

Transmembrane Prediction

Predict transmembrane spanning regions of proteins

Data Management

Integrated laboratory information management system for DNA barcoding

Dotmatics Platform Integration

Enables integration with Dotmatics Bioregister

GenBank Submission

Simplified submission of sequences, genomes, features, primers and traces

Recommended Resources

Plugin Development Kit

The Geneious Plugin Development Kit (PDK) allows you to take advantage of the Geneious Prime API to write your own plugins or workflows.

Wrapper Plugin Creator

Use the graphical wrapper plugin creator to run an existing command line program from inside Geneious Prime without writing any code

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