20.4 Geneious Server enabled plugins

This table details plugins which work with Geneious Server. Note that some of these plugins only run on Geneious Server and will not run locally on Geneious Prime.




Plugin Local Server






Geneious Alignment Yes Yes



MUSCLE Alignment Yes Yes



ClustalW Alignment Yes Yes



Realign Region Yes Yes



MAFFT Alignment Yes Yes



Consensus Align Yes Yes






Mauve Genome Yes Yes



LASTZ Alignment Yes Yes






Geneious Tree Builder Yes Yes



Consensus Tree Builder Yes Yes



MrBayes Yes Yes



PHYML Yes Yes



PAUP* Yes Yes



RAxML Yes No



GARLI Yes No



FastTree Yes No






Geneious Mapper Yes Yes



Geneious RNAseq Mapper Yes Yes



Bowtie/Bowtie 2 short read mapper Yes Yes



BBMap short read mapper Yes Yes



BWA short read mapper No Yes



Maq short read mapper No Yes



SOAP2 short read mapper No Yes



Tophat RNAseq aligner Yes Yes






Geneious de novo assembler Yes Yes



Velvet short read assembler Yes Yes



MIRA de novo assembler Yes Yes



Tadpole de novo assembler Yes Yes



SPAdes de novo assembler Yes Yes






Merge Paired Reads using BBMerge Yes Yes



Remove Duplicate Reads using BBTools Yes Yes



Trim using BBDuk Yes Yes



Remove Chimeric Reads Yes Yes



CustomBLAST Yes Yes