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 | 4.1.1 | Masks repeated sequences |
| RepeatModeler | 2.0.1 | de novo repeat masker | |
| Gene Prediction | Augustus | 3.4.0 | Eukaryotic gene predictor |
| BRAKER2 | 2.1.5 | Eukaryotic gene predictor | |
| GeneMarkES | 4.48 | Eukaryotic gene predictor | |
| GeneMarkS | 4.32 | Prokaryotic gene predictor | |
| Genscan | 1.0 | Eukaryotic gene predictor | |
| Glimmer3 | 3.0.2 | Prokaryotic gene predictor | |
| GlimmerM | 2.5.1 | Eukaryotic gene predictor | |
| SNAP | 11/29/2013 | Semi-HMM-based Nucleic Acid Parser, gene predictor | |
| Alignments | BLAST+ | 2.12.0 | Alignment tool for transcripts and proteins |
| pBLAT | 2.5 | Alignment tool for transcripts | |
| DIAMOND | 2.0.6 | Alignment tool for protein evidence | |
| HISAT2 | 2.2.1 | Aligns RNA-seq reads to genome | |
| PASA | 2.4.1 | 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 | 2.0.7 | Identifies tRNA sequences | |
| Consensus Gene Models | EVidenceModeler | 1.1.1 | Creates consensus gene structures for eukaryotes |
| Functional Annotation | BLAST+ | 2.12.0 | Alignment tool for proteins |
| DIAMOND | 2.0.6 | Alignment tool for proteins | |
| InterProScan | 5.53-87.0 | Classifies proteins by families and identifies functional domains | |
| Pfam | 1.6 | Uses Pfam database to identify functional domains and families in proteins | |
| SignalP | 5.0 | Predicts signal peptide cleavage sites in protein sequences | |
| TargetP | 2.0 | 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 | 5.2.2 | 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 |
