Geneious Prime Plugins

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

Write Your Own Plugins 

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

Alignment

Clustal Omega

Multiple sequence alignment using the latest addition to the Clustal family.

Download

André Marques

LASTZ

    Align large genomes using LASTZ

    Download

    MAFFT

      Fast and accurate multiple sequence alignment with MAFFT

      Download

      Mauve

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

        Download

        Aaron Darling

        SeqPartitioner

        Partition allele multisets from multiple alignments

        Download

        Jed Barlow

        Assembly

        BBDuk

          Adapter/Quality Trimming and Filtering

          Download

          BBMap

            Fast and sensitive aligner for RNA and DNA

            Download

            Bowtie

              Reference mapping with Bowtie

              Download

              CAP3

                Perform contig assembly using CAP3

                Download

                Contig Sorter

                  Sorts sequences in a contig according to the position of their first non-gap base.

                  Download

                  Biomatters Ltd.

                  FLASH

                  Merge paired sequencing reads using FLASH

                  Download

                  Dave O'Connor

                  Flye

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

                    Download

                    Minimap2

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

                      Download

                      MIRA

                      Efficient and accurate sequence assembly with MIRA

                      Download

                      Tophat

                        Fast splice junction mapping for RNA-Seq reads with TopHat

                        Download

                        Velvet

                          De novo assembly of short reads with Velvet

                          Download

                          Nucleotide Analysis

                          Augustus

                          Eukaryotic gene prediction with Augustus

                          Download

                          Michael Thon

                          Complement/Reverse

                          Complement or Reverse DNA sequences without doing both

                          Download

                          CpG Islands

                            Find targets for DNA methylation by predicting CpG islands

                            Download

                            Tobias Thierer

                            CRT

                            Find existing CRISPR sites in bacteria and archaea

                            Download

                            Dr Chris Duran

                            EMBOSS Nucleotide

                              Predict transcription factors and protein coding regions

                              Download

                              FreeBayes

                                Haplotype based variant finding with FreeBayes.

                                Download

                                Glimmer Prediction

                                  Predict genes in microbial DNA with Glimmer

                                  Download

                                  Heterozygotes

                                    Identify heterozygotes in chromatograms with secondary peak calling

                                    Download

                                    Microsatellites

                                      Streamlined microsatellite genotyping

                                      Download

                                      Mutate and Shuffle

                                        Automatically mutate or shuffle sequences

                                        Download

                                        Phobos

                                          Search genomes for tandem repeats / microsatellites using Phobos

                                          Download

                                          Dr Christoph Mayer

                                          Polymorphic SSRs

                                          Find polymorphic tandem repeats in alignments using Phobos

                                          Download

                                          Lars Smits

                                          Repeat Finder

                                            Find large, distant repeats

                                            Download

                                            Phylogenetics

                                            RAxML

                                              Fast maximum-likelihood tree building on large datasets with RAxML

                                              Download

                                              FastTree

                                                Fast phylogenetic tree building of huge datasets

                                                Download

                                                MrBayes

                                                  Bayesian phylogenetic analysis using MrBayes

                                                  Download

                                                  Prof. Marc Suchard

                                                  PAUP*

                                                    Phylogenetic inference using PAUP* 4.0

                                                    Download

                                                    PhyML

                                                      Phylogenetic inference for molecular evolution using PhyML

                                                      Download

                                                      DualBrothers

                                                        Identify recombination events in phylogenetic history with DualBrothers

                                                        Download

                                                        Prof. Marc Suchard

                                                        Species Delimitation

                                                        Assess putative species in phylogenetic trees

                                                        Download

                                                        Brad Masters et al.

                                                        Protein Analysis

                                                        Coiled Coils

                                                        Predict protein coiled coil regions

                                                        Download

                                                        Tobias Thierer

                                                        EMBOSS Protein

                                                          Predict secondary structure, antigenic regions and signal cleavage sites.

                                                          Download

                                                          EMBOSS Tools

                                                            Run several EMBOSS programs from within Geneious Prime

                                                            Download

                                                            Biomatters Ltd

                                                            InterProScan

                                                            Automatically annotate proteins with InterPro domains

                                                            Download

                                                            Michael Thon

                                                            PDB Structure Aligner

                                                              Structural alignment of PDB protein sequences

                                                              Download

                                                              Transmembrane

                                                                Predict transmembrane spanning regions of proteins

                                                                Download

                                                                Prof. Marc Suchard

                                                                Services and Searching

                                                                Biocode LIMS

                                                                Integrated laboratory information management system for DNA barcoding

                                                                Download

                                                                Dotmatics Platform Integration

                                                                  Enables integration with Dotmatics Bioregister.

                                                                  Download

                                                                  Find Big Folders

                                                                  List the size of all folders in your local database

                                                                  Download

                                                                  GenBank Submission

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

                                                                    Download

                                                                    Go To Documents

                                                                    Jump to documents by entering their unique IDs

                                                                    Download

                                                                    Groovy Console

                                                                    Opens a terminal window inside Geneious for scripting in the Groovy language

                                                                    Download

                                                                    Sequence Classifier

                                                                      Taxonomically classify samples against your own database of known sequences

                                                                      Download

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