]> GenBank Submission com.biomatters.plugins.genbanksubmission.GenbankSubmissionPlugin Geneious now supports uploading your sequences directly to GenBank. Simplify the process of submitting sequences, genomes, features, primers, traces, and more! Biomatters Ltd. Services and Searching Windows MacOS Linux https://assets.geneious.com/plugins/GenbankSubmission_1_2_4.gplugin - Improved user interface - Improved support for annotation types (e.g. support for RNA Editing) - Improved pre-submission error checking Windows MacOS Linux https://assets.geneious.com/plugins/GenbankSubmission_1_3_0.gplugin - Fixed bug causing submission to set molecule type to be "Genomic DNA" when choosing "Genomic RNA", "Ribosomal RNA" or " Transfer RNA" - GenBank submission now attempts to replace non-ascii character with equivalent ascii characters before submission - Will now submit existing LIMS sequences from reference assemblies generated by the Biocode LIMS plugin instead of generating new consensus sequences - Now correctly warns that alignments built from sequence lists are unsupported - Now warns if trying to submit a contig with too many reads - Remove "Split into separate sequences around '?' calls" consensus option to prevent crashes that occured when using it - Improved help button in GenBank Submission options for mac. - Now correctly allows non-mitochondrial genetic location when genetic code is set to "Candidate Division SR1 and Gracilibacteria Code" (translation table 25) - Updated for the NCBI's transition to HTTPS (http://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https) Windows MacOS Linux https://assets.geneious.com/plugins/GenbankSubmission_1_6_5.gplugin - Substitute any disallowed characters in the Submission Name with hyphens to prevent submission failure - Better error message if submission contains non-ASCII characters - Bundle Guava v30 library (previously depended upon Guava v25 from PrivateAPI) Windows MacOS Linux https://assets.geneious.com/plugins/GenbankSubmission_1_6_8.gplugin - Update tbl2asn to table2asn to use NCBI's newest validation command Windows MacOS Linux https://assets.geneious.com/plugins/GenbankSubmission_1_7_0.gplugin MrBayes mrbayes.plugin.MrBayesPlugin Runs the well known program <a href="http://mrbayes.csit.fsu.edu/">MrBayes</a> (included) for Bayesian estimation of phylogeny. Includes interactive display of posterior output. MrBayes is a standalone application and can also be run independently of Geneious. It is released under the <a href="http://www.gnu.org/copyleft/gpl.html">GNU General Public License</a>, and its source code is <a href="http://sourceforge.net/project/showfiles.php?group_id=129302">freely available</a>. Marc Suchard and Biomatters Ltd http://assets.geneious.com/plugins/img/MrBayes_small.png Phylogenetics - Compatibility with Geneious 5.1.1 and later Windows MacOS Linux https://assets.geneious.com/plugins/MrBayes_2_0_3.gplugin - Compatibility and stability improvements Windows MacOS Linux https://assets.geneious.com/plugins/MrBayes_2_0_5.gplugin - Improved memory efficiency - Forwards compatibility with Geneious 6.0 - Stopped MrBayes crashing when data has duplicate names Windows MacOS Linux https://assets.geneious.com/plugins/MrBayes_2_0_6.gplugin - Updated bundled binary to 3.2.1 - Added help for enabling CUDA/Beagle with custom binaries - Fix plugin not importing consensus tree produced by MrBayes - Properly display non-string attribute values produced by new MrBayes consensus tree - Better tip attributes for MrBayes consensus tree - Two MrBayes document types that had same name crashed workflows - make one type - Cancelling the operation in Geneious did not quit the running MrBayes process on Mac and Linux Windows MacOS Linux https://assets.geneious.com/plugins/MrBayes_2_0_9.gplugin - Fixed bug where MrBayes wouldn't run if there were Chinese characters in the path to the data directory - Improved NEXUS export performance for very long sequences - Added an option to skip importing raw trees to improve performance in cases where Geneious runs out of memory after running MrBayes Windows MacOS Linux https://assets.geneious.com/plugins/MrBayes_2_2_4.gplugin EMBOSS Tools com.biomatters.plugins.emboss.EmbossToolsPlugin Run several EMBOSS programs (included) from within Geneious including back translate, mutate, shuffle, garnier secondary structure prediction and more. <a href="http://emboss.sourceforge.net">EMBOSS</a> is a freely available software package for molecular biology. Biomatters Ltd Protein Nucleotide Fixed a bug that caused the charge graph to be drawn upside-down Windows MacOS Linux https://assets.geneious.com/plugins/EmbossTools_0_5_1_1.gplugin Fixed a bug that caused the charge graph to be drawn upside-down Windows MacOS Linux https://assets.geneious.com/plugins/EmbossTools_0_5_3.gplugin Added fuzznuc and fuzzpro Windows MacOS Linux https://assets.geneious.com/plugins/EmbossTools_0_6.gplugin Changes made to "Search for Motif with Mismatches" (fuzznuc and fuzzpro) - Added options for annotation type and name - Added the ability to search selected documents for all primers and probes - Fixed various bugs that could occur when searching over multiple documents Other changes - Completed support for operations on sequence list documents Windows MacOS Linux https://assets.geneious.com/plugins/EmbossTools_0_6_1.gplugin Mutate and Shuffle com.biomatters.plugins.mutateandshuffle.MutateAndShufflePlugin Automatically mutate or shuffle sequences Biomatters Ltd Nucleotide Protein Released as external plugin All https://assets.geneious.com/plugins/MutateAndShuffle_1_0_0.gplugin EMBOSS Protein Analysis com.biomatters.plugins.proteinanalysis.EMBOSSProteinAnalysisPlugin Predict secondary structure, antigenic regions and signal cleavage sites Biomatters Ltd Protein Released as external plugin All https://assets.geneious.com/plugins/EMBOSSProteinAnalysis_1_0_0.gplugin Fix occasional crash in sigcleave when the sequence starts with 'ID' All https://assets.geneious.com/plugins/EMBOSSProteinAnalysis_1_0_1.gplugin EMBOSS Nucleotide Analysis com.biomatters.plugins.nucleotideanalysis.EMBOSSNucleotideAnalysisPlugin Predict transcription factors and protein coding regions Biomatters Ltd Nucleotide - Fixed crash and/or incorrect results from protein prediction graph on sequences containing ? characters - Fixed failure to draw graph after choosing invalid options and then changing the options to be valid again - Fixed out of memory error with long error messages All https://assets.geneious.com/plugins/EMBOSSNucleotideAnalysis_1_1_1.gplugin Mauve Genome Alignment mauve.plugin.MauveAlignmentPlugin Construct and visualize multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Based on the freely available program <a href="http://darlinglab.org/mauve">Mauve</a>. Aaron Darling and Biomatters Ltd http://assets.geneious.com/plugins/img/Mauve_small.png Alignment Upgraded Mauve to version 2.1.1 Windows MacOS Linux https://assets.geneious.com/plugins/MauveGenomeAlignment_0_5.gplugin - Improved support for importing xmfa files - Fixed crash when clicking on Alignment Windows MacOS Linux https://assets.geneious.com/plugins/MauveGenomeAlignment_0_6_7.gplugin - Added support for sequence lists - Better progress indication - Compatible with Geneious 4.8 Windows MacOS Linux https://assets.geneious.com/plugins/MauveGenomeAlignment_0_6_8.gplugin Supports annotation tracks Windows MacOS Linux https://assets.geneious.com/plugins/MauveGenomeAlignment_0_6_11.gplugin - Fixed a problem where import fails on valid XMFA file when there is no space in front of sequence number - Fixed the importer producing nameless documents - Made the operation failed dialogues more friendly - Fixed a problem that caused alignments extracted from features in the genome alignment viewer to be offset by 1 - Fixed a problem where question mark nucleotides were being deleted by Mauve and causing annotations to be offset - Now mentions when no alignment could be produced All https://assets.geneious.com/plugins/MauveGenomeAlignment_1_0_5.gplugin - Fixed DCJ analysis in most cases - Added an option to save contigs in order as a sequence list or concatenated sequence when running MCM - Mauve alignment exporter now exports referenced source genomes in Genbank flat format (better supported by current versions of Mauve) - Mauve .backbone file is now saved; when exporting Mauve alignments in .xmfa format the .backbone file will also be exported if it is available All https://assets.geneious.com/plugins/MauveGenomeAlignment_1_1_1.gplugin - Fixed a bug loading of annotations and contig boundaries for sequence lists missing accession numbers on contained sequences - Updated some icons to be high res and fit the new UI. - Tweak wording of "Show Details" in exception dialog - Bundle Guava v30 library (previously depended upon Guava v25 from PrivateAPI) - Prevent creating or viewing invalid alignments All https://assets.geneious.com/plugins/MauveGenomeAlignment_1_1_3.gplugin PAUP* com.biomatters.plugins.paup.PaupPlugin Run <a href="https://paup.phylosolutions.com">PAUP*</a> phylogenetic inference from inside Geneious. You will need a licensed copy of PAUP*, or an active <a href="http://phylosolutions.com/paup-test/">alpha-test release</a> to use this plugin. Includes Modeltest. Modeltest is covered by the GPL. <a href="http://desktop-links.geneious.com/assets/libraries/modeltest3.7.zip">Download</a> the Modeltest source. Biomatters Ltd Phylogenetics All https://assets.geneious.com/plugins/Paup_1_3_3.gplugin PhyML fr.lirmm.PHYML.PHYMLPlugin Maximum Likelihood tree building for alignments. Please cite Guindon S. & Gascuel O. (2003) Syst. Biol. 52:696-704. when using PHYML. Vincent Lefort and Biomatters Ltd Phylogenetics Fixed crash caused by progress reporting All https://assets.geneious.com/plugins/PhyML_1_0.gplugin - Added custom substitution model option, can be used with ModelTest output - Added optimization option (Topology/Length/Rate) All https://assets.geneious.com/plugins/PhyML_2_1_0.gplugin - Fixed crash on Windows when running from a data directory containing certain non-Latin characters (e.g., Chinese) - Fixed crash that would occur when running with a custom substitution model on Windows machines All https://assets.geneious.com/plugins/PhyML_2_2_3.gplugin - Updated included PhyML to version 3.3.20180621 - Show PhyML version number in the options dialog All https://assets.geneious.com/plugins/PhyML_2_2_4.gplugin Transmembrane Prediction org.suchard.membrane.MembranePredictionPlugin Predicts transmembrane spanning regions of proteins using TMHMM (Transmembrane Hidden Markov model). Reference: Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information; Håkan Viklund and Arne Elofsson; Protein Science Vol. Protein Sci. 2004 Jul;13(7):1908-17. Marc Suchard and Biomatters Ltd Protein - More informative annotations Windows MacOS Linux https://assets.geneious.com/plugins/Transmembrane_Prediction_0_7.gplugin Replace Windows binaries with newly-built copies that can output posterior probabilities Windows MacOS Linux https://assets.geneious.com/plugins/Transmembrane_Prediction_1_0_1.gplugin Fixes crash when sequence name is empty. Windows MacOS Linux https://assets.geneious.com/plugins/Transmembrane_Prediction_1_0_2.gplugin Heterozygotes com.biomatters.plugins.heterozygote.HeterozygotePlugin Identifies heterozygotes in sequences with trace information by looking at the relative height of traces at peak positions. Biomatters Ltd Nucleotide - Now works on alignments and contigs All https://assets.geneious.com/plugins/Heterozygotes_1_2.gplugin - Allow configuration of options when running from workflow - Fixed false positives - Fixed false negatives - Added new setting ("Peak Detection Height") for finer grained tweaking of heterozygote detection - Added new setting ("Minimum confidence to call heterozygote") to prevent heterozygote detection in low quality regions - Renamed "Minimum Confidence Score" to "Flag all positions with confidence below" to better reflect what that setting does. - Added setting "Identify incorrect base calls when alternative peak height is" to detect clearly wrong base call All https://assets.geneious.com/plugins/Heterozygotes_2_0_0.gplugin Coiled Coils com.biomatters.plugins.coiledCoils.CoiledCoilsPlugin A protein sequence graph for predicting coiled-coil regions based on "Predicting coiled-coil regions in proteins", Andrei Lupas. Curr Opin Struct Biol. 1997 Jun;7(3):388-93. Tobias Thierer and Biomatters Ltd Protein - Now gives identical results to coils2 - Fix issue with sequences with fewer than 28 residues All https://assets.geneious.com/plugins/Coiled_Coils_1_1_1.gplugin CpG Islands com.biomatters.plugins.cpgIslands.CpgIslandsPlugin A nucleotide sequence graph for predicting CpG Islands based on the model and parameterisation described by Richard Durbin, Sean Eddy et al. (1999) in Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Tobias Thierer and Biomatters Ltd Nucleotide - Improved graph drawing on circular sequences in Geneious 4.0+ All https://assets.geneious.com/plugins/CpG_Islands_1_1.gplugin Complement Or Reverse Only com.biomatters.plugins.ComplementOrReverseOnly.ComplementOrReverseOnlyPlugin Provides menu items to 'Complement Only' or 'Reverse Only' a sequence. Biomatters Ltd Nucleotide Fixed Bug to make it compatible with Geneious 8 All https://assets.geneious.com/plugins/ComplementOrReverseOnly_1_1.gplugin Batch Rename com.biomatters.plugins.batchRename.BatchRenamePlugin Permanently rename sets of documents using the values from another column such as Organism Biomatters Ltd Misc All https://assets.geneious.com/plugins/BatchRename_1_0.gplugin Phobos Tandem Repeat Finder com.biomatters.plugins.phobos.PhobosPlugin Finds tandem repeats in DNA sequences using <a href="http://www.ruhr-uni-bochum.de/spezzoo/cm/cm_phobos.htm">Phobos 3.3.10</a>. Biomatters Ltd and Dr Christoph Mayer Nucleotide All https://assets.geneious.com/plugins/Phobos_1_0_6.gplugin PDB Structure Aligner com.biomatters.plugins.structureAlign.StructureAlignPlugin Aligns two PDB structures using BioJava structure alignment. Biomatters Ltd. Protein Fixed an issue with multi-model structures All https://assets.geneious.com/plugins/StructureAlign_0_5.gplugin Species Delimitation speciesDelimitation.SpeciesDelimitationPlugin Explore species properties on a phylogenetic tree, including the chance probability of distinctive clades and the reliability of species identification. Brad Masters (major developer) and Howard Ross (modifications) http://assets.geneious.com/plugins/3rdparty/SpeciesDelimitation_small.png Phylogenetics Fixed typo that led to crashes if an error occurred during results table creation All https://assets.geneious.com/plugins/3rdparty/SpeciesDelimitation_1_4_5.gplugin MAFFT multiple aligner com.biomatters.plugins.mafft.MafftPlugin Align sequences using the program <a href="http://mafft.cbrc.jp/alignment/software/">MAFFT</a> which features several methods for extremely fast and accurate alignment. Biomatters Ltd. Alignment - 64-bit support on Windows - Further compatibility fixes on Windows All https://assets.geneious.com/plugins/Mafft_1_1.gplugin - Updated binary to 7.017 All https://assets.geneious.com/plugins/Mafft_1_3.gplugin - Handle network file paths on Windows - Add option to automatically determine sequences' direction - Fix error in Windows 64 version handling of spaces in data directory path All https://assets.geneious.com/plugins/Mafft_1_3_3.gplugin - Handle out of memory error gracefully instead of with crash - Update binary to 7.308/7.309 All https://assets.geneious.com/plugins/Mafft_1_3_6.gplugin - Update MAFFT to 7.450 (7.429 for Window 32-bit) - fixes issues running MAFFT on Windows when paths contain non-Latin-1 characters - Add support for using multiple threads (--thread -1) All https://assets.geneious.com/plugins/Mafft_1_4_0.gplugin - Update MAFFT to 7.490 - Removed support for MAFFT under win32 All https://assets.geneious.com/plugins/Mafft_1_5_0.gplugin InterProScan com.michaelrthon.geneiousplugins.interproscan.InterproscanPlugin Search InterPro, an integrated database of protein signatures Michael Thon and Biomatters Protein - Fixed InterProScan by using a new REST API Windows Linux https://assets.geneious.com/plugins/InterProScan_2_1_0.gplugin - Fixed InterProScan by using a new REST API MacOS https://assets.geneious.com/plugins/InterProScan_2_1_0.gplugin Glimmer Gene Prediction com.biomatters.plugins.glimmer.GlimmerPlugin Predict genes using Glimmer3. <a href="http://www.cbcb.umd.edu/software/glimmer/">Glimmer</a> is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Biomatters Ltd. Nucleotide Improved error handling to track down issues with Glimmer on certain data All https://assets.geneious.com/plugins/Glimmer_1_3.gplugin -Improved memory efficiency -Fixed parse error All https://assets.geneious.com/plugins/Glimmer_1_4.gplugin - Fixed the plugin so it will work on Windows - Made it fail gracefully on training annotations that Glimmer is unable to process - Fixed cryptic failure messages on some sequences - Fixed a crash when the Glimmer model output contains an empty line All https://assets.geneious.com/plugins/Glimmer_1_5.gplugin Microsatellite Plugin com.biomatters.plugins.microsatellite.MicrosatellitePlugin Import ABI .fsa files, automatically call peaks and fit ladders, bin data into alleles and export for further analysis. Biomatters Ltd. Nucleotide - Added more ladders - Ladders are now stored in an editable text file All https://assets.geneious.com/plugins/Microsatellite_1_2_0.gplugin - Fix some crashes in bin guessing - Fix resource leak (threads not terminated) - Fix occasional crash in notification slider animation All https://assets.geneious.com/plugins/Microsatellite_1_4_0.gplugin - Fix a crash due to rounding error that could happen when a bin midpoint is exactly at a ladder peak - Fix a crash when loading FSA files with more than 5 traces - Fix quirky scrolling behaviour with Apple magic mouse or trackpad - Bundle Guava v30 library (previously depended upon Guava v25 from PrivateAPI) All https://assets.geneious.com/plugins/Microsatellite_1_4_7.gplugin Cap3 com.biomatters.plugins.cap3.Cap3Plugin Performs contig assembly using CAP3 (http://seq.cs.iastate.edu) Lars Smits and Biomatters Ltd. Assembly All https://assets.geneious.com/plugins/Cap3_1_0.gplugin Polymorphic SSRs com.biomatters.plugins.polymorphicSsr.PolymorphicSSRPlugin Find polymorphic tandem repeats in an alignment using Phobos Lars Smits and Biomatters Ltd. Nucleotide All https://assets.geneious.com/plugins/PolymorphicSSR_1_0.gplugin RAxML RAxML RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. Biomatters Ltd. Phylogenetics All https://assets.geneious.com/plugins/RAxML_1_0.gplugin - Added link to RAxML website - Added citation information for RAxML All https://assets.geneious.com/plugins/RAxML_4_0.gplugin FastTree FastTree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. Biomatters Ltd. Phylogenetics All https://assets.geneious.com/plugins/FastTree_2_1_12.gplugin FreeBayes Variant Finder FreeBayes_Variant_Finder Find variants using <a href="https://github.com/ekg/freebayes">FreeBayes</a> Biomatters Ltd. Nucleotide All https://assets.geneious.com/plugins/FreeBayes_Variant_Finder_1_0.gplugin - Upgraded FreeBayes to version 1.1 All https://assets.geneious.com/plugins/FreeBayes_Variant_Finder_1_1_0.gplugin Bowtie com.biomatters.plugins.bowtie.BowtiePlugin Bowtie is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. The plugin includes both <a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml">Bowtie2</a> and <a href="http://bowtie-bio.sourceforge.net/index.shtml">Bowtie</a>. Only 64 bit operating systems are supported. Bowtie2 is released under the <a href="https://www.gnu.org/copyleft/gpl.html">GNU General Public License v3</a>, and its source code is <a href="https://github.com/BenLangmead/bowtie2">freely available</a>. Biomatters Ltd. Assembly - Removed the debug executables for Windows which were required for Bowtie2 2.2.6 - Upgraded Bowtie2 to 2.3.0 on Windows, 2.3.2 on Linux and MacOS All https://assets.geneious.com/plugins/Bowtie_7_2_1.gplugin - Improved Bowtie command line parameters help - Upgraded Bowtie2 to 2.4.5 All https://assets.geneious.com/plugins/Bowtie_7_2_2.gplugin LASTZ com.biomatters.plugins.lastz.LastZPlugin LASTZ is a BLAST-like alignment tool for the pairwise alignment of chromosome-sized nucleotide sequences. It results in a modified Sequence Document viewer showing a dotplot graph above the target sequence. Many query sequences can be aligned against a single target, allowing researchers to find the distribution of their sequence of interest in the query sequences/genome. Biomatters Ltd. Alignment - Fixed occasional crash in progress dialog trying to display a warning All https://assets.geneious.com/plugins/LASTZ_7_0_2.gplugin - Updated LastZ to version 1.04.15 All https://assets.geneious.com/plugins/LASTZ_7_0_3.gplugin Velvet com.biomatters.plugins.velvet.VelvetPlugin Performs contig assembly using Velvet. See <a href="http://www.ebi.ac.uk/~zerbino/velvet/">http://www.ebi.ac.uk/~zerbino/velvet/</a>. Biomatters Ltd. Assembly - Upgrade to Velvet 1.2.10 - Implement on desktop Geneious on all 64-bit platforms All https://assets.geneious.com/plugins/Velvet_7_0.gplugin Fixed crash when there are 0 length reads and all other reads are shorter than 46 All https://assets.geneious.com/plugins/Velvet_7_0_4.gplugin MIRA com.biomatters.plugins.mira.MiraPlugin Multi-pass DNA sequence assembler for whole genome and EST/RNASeq. Biomatters Ltd. Assembly - Release open source version of plugin - Nicer failure message when trying to run MIRA on sequences without quality - Make compatible with Geneious 10.1 and newer All https://assets.geneious.com/plugins/Mira_1_1_1.gplugin Fixes incompatible locale settings preventing MIRA from running on Ubuntu out of the box. All https://assets.geneious.com/plugins/Mira_1_1_2.gplugin Classify Sequences com.biomatters.plugins.classifySequences.ClassifySequencesPlugin Classifies one or more sequences by comparing to a known database Aaron Kennedy (USDA-APHIS-PPQ) and Biomatters Services and Searching Updated author to include Aaron Kennedy (USDA-APHIS-PPQ) All https://assets.geneious.com/plugins/SequenceClassifier_1_1.gplugin - Updated for compatibility only with versions of Geneious Prime 2019.0 and later All https://assets.geneious.com/plugins/SequenceClassifier_1_1_1.gplugin Barcode Validator com.biomatters.plugins.barcoding.validator.research.BarcodeValidatorPlugin Runs batch validation on sets of traces and barcode sequences against user specified parameters. Biomatters Ltd Services and Searching - Exposed options for the MUSCLE alignment that occurs during PCI calculation - Made the report more compatible between versions of Geneious All https://github.com/Biomatters/barcode-validator/releases/download/v1.0.1/BarcodeValidator_1_0_1.gplugin Biocode Plugin com.biomatters.plugins.biocode.BiocodePlugin The Biocode LIMS is a Geneious plugin that was developed as part of the Moorea Biocode Project. It comprises everything you need to manage your lab and sequence analysis workflows. Biocode Services and Searching 3.0.7
- Set default geome fims instance to production
- Enable either production or develop geome to be called
- Bug fixes

3.0.6
- Enable queries on GeOMe project (in the drop-down list of search terms)
- Cache FIMS data when performing tissueID search in GeOMe. Eliminates need to redo the search
- Specify a single query for all available projects rather than looping projects for GeOMe
- Populate attributes using a call to GeOMe network API instead of individual projects which speeds up populating attributes.
- Enable full-text queries for GeOMe projects.]]> All https://github.com/biocodellc/biocode-lims/releases/download/v3.0.7/BiocodePlugin_3_0_7.gplugin FLASH FLASH FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data. Dave O'Connor Assembly - Exposed more options - Added custom command line - Improved descriptions All https://assets.geneious.com/plugins/FLASH_1_1.gplugin BBDuk Trimmer com.biomatters.plugins.bbduk.BBDukPlugin Adapter/Quality Trimming and Filtering using BBDuk from BBTools by Brian Bushnell. As of Geneious Prime 2023 this plugin is no longer required to access the BBDuk functionality. Biomatters Ltd. Assembly All https://assets.geneious.com/plugins/BBDuk_1_0.gplugin BBMap com.biomatters.plugins.bbmap.BBMapPlugin BBMap short read aligner from BBTools by Brian Bushnell Biomatters Ltd. Assembly All https://assets.geneious.com/plugins/BBMap_1_0.gplugin Repeat Finder com.biomatters.plugins.repeatFinder.RepeatFinderPlugin Identifies regions in one or more sequences that are repeated elsewhere in the sequences. Biomatters Ltd. Nucleotide All https://assets.geneious.com/plugins/RepeatFinder_1_0.gplugin - Updated for compatibility only with versions of Geneious Prime 2019.0 and later All https://assets.geneious.com/plugins/RepeatFinder_1_0_1.gplugin Augustus com.michaelrthon.augustusPlugin.AugustusPlugin Augustus is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. This plugin allows you to choose an organism then run Augustus and save the results as annotations on your sequence. Mike Thon http://assets.geneious.com/plugins/3rdparty/augustus.png Nucleotide - Augustus can now be configured from workflows All https://assets.geneious.com/plugins/3rdparty/Augustus-0.1.1.gplugin Minimap2 Minimap2 A versatile mapper / pairwise aligner for genomic and spliced nucleotide sequences Biomatters Ltd. Assembly All https://assets.geneious.com/plugins/Minimap2_1_0_0.gplugin Updates minimap2 to version 2.24. All https://assets.geneious.com/plugins/Minimap2_2_1_0.gplugin Updates minimap2 to version 2.29. All https://assets.geneious.com/plugins/Minimap2_2_2_0.gplugin Flye Flye A de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies Biomatters Ltd. Assembly Fixes crash with python 3.8 on Mac. All https://assets.geneious.com/plugins/Flye_1_3.gplugin Use bundled python interpreter on MacOS to avoid relying on system python MacOS https://assets.geneious.com/plugins/Flye_1_3_1.gplugin Update to Flye 3.0.5 to fix issue with importing when running minimap2. All https://assets.geneious.com/plugins/Flye_1_3_2.gplugin