Available Tools

The below table lists the tools that have been integrated into GenSAS.  Click on the tool name to be redirected to the tool website and documentation.  We are working on updating many of the tools to the most current version.  Click here for file with GenSAS tool and database references.

Category Tool Name Version Description
Repeat Masking RepeatMasker 4.0.7 Masks repeated sequences
RepeatModeler 1.0.11 de novo repeat masker
Gene Prediction Augustus 3.3.1 Eukaryotic gene predictor
BRAKER2 2.1.1 Eukaryotic gene predictor
GeneMarkES 4.33 Eukaryotic gene predictor
GeneMarkS 4.32 Prokaryotic gene predictor
Genscan 1.0 Eukaryotic gene predictor
Glimmer3 3.02 Prokaryotic gene predictor
GlimmerM 2.5.1 Eukaryotic gene predictor
SNAP 11/29/2013 Semi-HMM-based Nucleic Acid Parser, gene predictor
Alignments BLAST+ 2.7.1 Alignment tool for transcripts and proteins
BLAT 35 Alignment tool for transcripts
DIAMOND 0.9.22 Alignment tool for protein evidence
HISAT2 2.1.0 Aligns RNA-seq reads to genome
PASA 2.3.3 Aligns EST or transcript evidence
TopHat 2.1.1 Aligns RNA-seq reads to genome
Genomic Features Getorf EMBOSS-6.6.0 Open reading frame finder
RNAmmer 1.2 Finds rRNA sequences
SSR Finder N/A Finds user defined simple sequence repeats
tRNAScan-SE 2.0 Identifies tRNA sequences
Consensus Gene Models EVidenceModeler 06/25/2012 Creates consensus gene structures for eukaryotes
Functional Annotation BLAST+ 2.6.0 Alignment tool for proteins
DIAMOND 0.9.22 Alignment tool for proteins
InterProScan 5.24-63.0 Classifies proteins by families and identifies functional domains
Pfam 1.5 Uses Pfam database to identify functional domains and families in proteins
SignalP 4.1 Predicts signal peptide cleavage sites in protein sequences
TargetP 1.1 Predicts the subcellular location of eukaryotic proteins based on signal peptide sequences
Genome Browser Apollo 2.0.7 Annotation editor
JBrowse 1.12.1 Genome browser
Assembly/annotation metrics BUSCO 3.0.2 Determines genome assembly and annotation completeness based on orthologs
One code to find them all 1.0 Reports repeat types from RepeatMasker
PRINSEQ-lite 0.20.4 Used to analyze assembly file for sequence number and size