Table 1.
Biopipe Runnables
|
Modules (Bio::Pipeline::Runnable::*) |
Class |
|---|---|
| BLAST | General alignment |
| Blat | Fast sequence alignment |
| DNA Block Aligner | Sensitive DNA alignment |
| Eponine | Transcription start site finder |
| Est2Genome | EST to genomic sequence alignment |
| Fasta | Fasta suite of alignment programs that include fasta, tfastx-fasty |
| Genewise | Homology-based gene prediction |
| Genscan | Ab initio gene prediction |
| Molphy | Molecular phylogenetics package |
| MSA | Multiple sequence alignment programs like CLUSTALW and Tcoffee |
| PAML | Phylogenetic analysis by maximum likelihood package |
| PHYLIP | PHYLIP package programs that include consense, drawgram, drawtree, neighbor, protdist, protpars, and seqboot |
| Primate | Short oligo search |
| Promoterwise | Sensitive alignment for promoter sequences |
| ProteinAnnotation | Suite of protein annotation programs that includes Seg, Coils, Hmmpfam, FingerPrintScan, PFScan, Signalp, Tmhmm |
| Pseudowise | Pseudo gene predictor |
| RepeatMasker | Interspersed repeat finder |
| Sim4 | CDNA to genomic sequence alignment |
| TribeMCL
|
Protein family clustering
|
-
A snapshot of the list of runnables available in Biopipe. These runnables serve as an interface between the wrappers and the pipeline system
