| Analysis | Module representing any (remote or local)
analysis tool |
| AnalysisFactory | A directory of analysis tools |
| AssemblerBase | base class for wrapping external assemblers |
| BEDTools | Run wrapper for the BEDTools suite of programs *BETA* |
| BWA | Run wrapper for the BWA short-read assembler *BETA* |
| BlastPlus | A wrapper for NCBI's blast+ suite |
| Bowtie | Run wrapper for the Bowtie short-read assembler *BETA* |
| Cap3 | wrapper for CAP3 |
| Coil | wrapper for ncoils program |
| EMBOSSApplication | class for EMBOSS Applications |
| EMBOSSacd | class for EMBOSS Application qualifiers |
| ERPIN | Wrapper for local execution of the ERPIN suite of
programs. |
| Ensembl | A simplified front-end for setting up the registry
for, and then using an Ensembl database with the
Ensembl Perl API. |
| Eponine | Object for execution of the Eponine which
is a mammalian TSS predictor |
| FootPrinter | wrapper for the FootPrinter program |
| Genemark | Wrapper for local execution of the GeneMark
family of programs. |
| Genewise | Object for predicting genes in a
given sequence given a protein |
| Genscan | Object for identifying genes in a
given sequence given a matrix(for appropriate organisms). |
| Glimmer | Wrapper for local execution of Glimmer,
GlimmerM and GlimmerHMM. |
| Hmmer | Wrapper for local execution of hmmalign, hmmbuild,
hmmcalibrate, hmmemit, hmmpfam, hmmsearch |
| Infernal | Wrapper for local execution of cmalign, cmbuild,
cmsearch, cmscore |
| Job | |
| MCS | Wrapper for MCS |
| Maq | Run wrapper for the Maq short-read assembler *BETA* |
| Match | Wrapper for Transfac's match(TM) |
| Mdust | Perl extension for Mdust nucleotide filtering |
| Meme | Wrapper for Meme Program |
| Minimo | Wrapper for local execution of the Minimo assembler |
| Newbler | Wrapper for local execution of Newbler |
| Phrap | a wrapper for running Phrap |
| Primate | for Primate, Guy Slater's near exact match finder for short sequence
tags. |
| Primer3 | Create input for and work with the output
from the program primer3 |
| Prints | Bio::Tools::Run::Prints |
| Profile | Bio::Tools::Run::Profile |
| Promoterwise | Wrapper for aligning two sequences using
promoterwise |
| Pseudowise | Object for prediting pseudogenes in a
given sequence given a protein and a cdna sequence |
| RNAMotif | Wrapper for local execution of rnamotif, rm2ct,
rmfmt, rmprune |
| RepeatMasker | Wrapper for RepeatMasker Program |
| Samtools | a run wrapper for the samtools suite *BETA* |
| Seg | Object for identifying low complexity
regions in a given protein seequence. |
| Signalp | Bio::Tools::Run::Signalp |
| Simprot | Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree |
| StandAloneBlastPlus(1) | Compute with NCBI's blast+ suite *ALPHA* |
| TigrAssembler | Wrapper for local execution of TIGR Assembler
v2 |
| Tmhmm | Object for identifying transmembrane helixes
in a given protein seequence. |
| TribeMCL | Bio::Tools::Run::TribeMCL |
| Utils | |
| Vista | for Vista |
| tRNAscanSE | Wrapper for local execution of tRNAscan-SE |
| Amap | Object for the calculation of an
iterative multiple sequence alignment from a set of unaligned
sequences or alignments using the Amap (2.0) program |
| Blat | Bio::Tools::Run::Alignment::Blat |
| Clustalw(2) | Object for the calculation of a
multiple sequence alignment from a set of unaligned sequences or
alignments using the Clustalw program |
| DBA | Object for the alignment of two
sequences using the DNA Block Aligner program. |
| Exonerate | Bio::Tools::Run::Alignment::Exonerate |
| Gmap | Wrapper for running gmap. |
| Kalign | Object for the calculation of an
iterative multiple sequence alignment from a set of unaligned
sequences or alignments using the KALIGN program |
| Lagan | Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments) |
| MAFFT | run the MAFFT alignment tools |
| MSAProbs | Object for the calculation of a
multiple sequence alignment (MSA) from a set of unaligned sequences using
the MSAProbs program |
| Muscle(2) | Object for the calculation of an
iterative multiple sequence alignment from a set of unaligned
sequences or alignments using the MUSCLE program |
| Pal2Nal | Wrapper for Pal2Nal |
| Probalign | Object for the calculation of
a multiple sequence alignment from a set of unaligned sequences or
alignments using the Probalign program |
| Probcons(2) | Object for the calculation of an
iterative multiple sequence alignment from a set of unaligned
sequences or alignments using the Probcons program |
| Proda | Object for the calculation of sets
of multiple sequence alignments from a set of unaligned sequences or
alignments using the Proda program. |
| Sim4 | Wrapper for Sim4 program that allows
for alignment of cdna to genomic sequences |
| StandAloneFasta | Object for the local
execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3
ssearch3) |
| TCoffee(2) | Object for the calculation of a
multiple sequence alignment from a set of unaligned sequences or
alignments using the TCoffee program |