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.

Category Tool Name Description
Repeat Masking RepeatMasker Masks repeated sequences
RepeatModeler de novo repeat masker
Gene Prediction Augustus Eukaryotic gene predictor
GeneMarkES Eukaryotic gene predictor
GeneMarkS Prokaryotic gene predictor
Genscan Eukaryotic gene predictor
Glimmer3 Prokaryotic gene predictor
GlimmerM Eukaryotic gene predictor
SNAP Semi-HMM-based Nucleic Acid Parser, gene predictor
Alignments BLAST Alignment tool for transcripts and proteins
BLAT Alignment tool for transcripts
PASA Aligns EST or transcript evidence
TopHat Aligns RNA-seq reads to genome
Genomic Features Getorf Open reading frame finder
RNAmmer Finds rRNA sequences
SSR Finder Finds user defined simple sequence repeats
tRNAScan-SE Identifies tRNA sequences
Consensus Gene Models EVidenceModeler Creates consensus gene structures for eukaryotes
Functional Annotation InterProScan Classifies proteins by families and identifies functional domains
Pfam Uses Pfam database to identify functional domains and families in proteins
SignalP Predicts signal peptide cleavage sites in protein sequences
TargetP Predicts the subcellular location of eukaryotic proteins based on signal peptide sequences
BLAST Alignment tool for proteins
Genome Browser Apollo Annotation editor
JBrowse Genome browser