de novo
- PRICE 1.0.1 – de novo Genome Assembler
- ABySS 1.3.5 – de novo, parallel, paired-end Sequence Assembler
- Multi-Dendrix 1.0 – Multiple Pathway De novo Driver Exclusivity
- SMART TOOLS – Implementation of a de novo Genome-wide Computational approach for updating Brachypodium miRNAs
- Edena v3 dev130110 – De Novo Short Reads Assembler
- W-ChIPMotifs – de novo Motif Discovery from ChIP-based High throughput data
- VICUNA 1.1 – de novo Assembler for Ultra-deep Sequence data
- AV454 1.0 – de novo Consensus Assembler designed for reads derived from diverse Viral Populations
- GibbsModule – Multispecies de novo Identification of Cis-regulatory Motifs and Modules
- DeNovo Pipeline 1.4.2 – Protein Identification by de novo Interpretation
- QSRA 1.0 – Quality-value guided de novo Short Read Assembler
- LTRsift 1.0.1 – Postprocessing of de novo predicted LTR Retrotransposon Annotations
- Tag-DB 0.4.0 – de novo Sequencing and Tag-based database Searching of MS/MS Spectra
- MAP 20121108 – A de novo Metagenomic Assembly program for Shotgun DNA reads
- SeqCons 1.0 – de novo and reference-guided Sequence Assembly
- Pasqual 1.0 – Parallel de Novo Genome Sequence Assembler
- INVERTER – de novo Tandem Repeat finder
- Meta-IDBA 0.19 – De Bruijn Graph De Novo short read assembler designed for de novo Metagenomic Assembly
- T-IDBA 0.20 – De Bruijn Graph De Novo Short Read Assembler for Transcriptome
- IDBA-UD 1.09 – De Bruijn Graph De Novo Assembler with Highly Uneven Sequencing Depth
- IDBA 0.20 – De Bruijn Graph De Novo Assembler for sequence assembly
- GS De Novo Assembler – de novo DNA Sequence Assembly
- Oases 0.2.08 – De novo Transcriptome Assembler for very short reads
- RepeatModeler 1.0.5 – de-novo Repeat Family Identification and Modeling package
- PepNovo 20120423 – De novo Sequencing of low Precision MS/MS Data
- MSNovo 5.0 – de novo Peptide Sequencing program for Tandem Mass Spectrometry
- WEAV 0.2 – de novo Assembly program for both Genome and RNA
- SHORTY 2.0 – de novo Assembler
- CisModule 20051205 – De novo Discovery of Cis-regulatory Modules
- MultiModule 1.0 – de novo Discovery of Cis-regulatory Modules in Multiple Species
- LutefiskXP 1.0.7 / Lutefisk – De novo Interpretation of Peptide CID Cpectra
- Anchor 0.3.1 – Post-processing Tools for de novo Assemblies
- HHrepID 1.0.0 – de novo Protein Repeat Detection
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