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

20.4 Geneious Server enabled plugins