GCP -SP4 Community Programs
CIP PROGRAMS
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Program
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Run program
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Users
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| BioView Workbench | Paracel Blast | Roland Schafleitner, Rosalina Tincopa | |
| Multi-locus Genotype | Structure(video-demo) | Elisa Mihovilovich | |
| Statistic Software | R Statistic(video-demo) | Run | Reinhard Simon |
| Annotation of Sequences | Blast2go | Roland Schafleitner | |
| Cleaning of nucleotide sequence | Repeatmasker | Roland Schafleitner, Rosalina Tincopa | |
| Seqclean | Roland Schafleitner, Rosalina Tincopa | ||
| Assembly of nucleotide sequence | CAP3 | Roland Schafleitner, Rosalina Tincopa | |
| MIRA | Roland Schafleitner, Rosalina Tincopa | ||
| TGICL | Roland Schafleitner, Rosalina Tincopa | ||
| Vcake | Jan Kreuze, Wilmer Cuellar | ||
| Ssake | Jan Kreuze, Wilmer Cuellar | ||
| Velvet | Jan Kreuze, Wilmer Cuellar | ||
| Mapping and Assembly with Quality | Maq | Jan Kreuze, Wilmer Cuellar |
ICRISAT Programs
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Program
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Run program
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Users
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| Population Genetics | Web Structure | Run | Ramu, Shamshad Alam |
| Assembly | Cap3 | Run | Mahendar, Pavana, Spurthi, NLRaju, Anuja,Rajaram |
| estassemblyprogram | Run | Pavana, Spurthi, NLRaju | |
| NGSmapping/assembly | Maq | Vivek | |
| Novoalign | Vivek | ||
| Mosaik | Vivek | ||
| Velvet | Vivek | ||
| miRNA identification | MiRScan | Vivek | |
| RNAfold | Vivek | ||
| Sequence Aligment | Blastpar (Paracel-blast) | Run | Mahendar,Pavana,Spurthi,NLRaju,Ramu, Rajaram |
| Fasta | Run | Pavana, NLRaju | |
| Pattern scanning | scan_for_matches | Vivek | |
| Data manipulation | imisa | Run | Rajaram |
| misa | Run | Mahendar, Pavana, Spurthi, NLRaju, Anuja, Ramu |
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| snp2caps | Run | Pavana, Spurthi, NLRaju, Shamshad Alam, Anuja, Neha |
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| unigene | Run | Pavana, NLRaju | |
| Format parsing | blastparser | Run | Pavana, NLRaju, Ramu, Rajaram |
| cap3_convert | Run | Pavana, NLRaju, Rajaram | |
| clustalw_convert | Run | Pavana, NLRaju | |
| SNP Statistics | SNP_diversity_estimator | Run | Pavana, Spurthi, NLRaju, Shamshad Alam, Anuja, Ashutosh |
| Quant. gene expresion | R Statistic | Pavana, NLRaju |
IRRI Programs
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Program
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Run program
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Users
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| Sequence analysis | EMBOSS | Ramil Mauleon, Richard Bruskiewich | |
| Statistical analysis of microarray data | R with Bioconductor package suite | Ramil Mauleon, Violeta Bartolome | |
| Cleanup of nucleotide sequences | Repeatmasker | Victor Jun Ulat | |
| Finding cis element motif in gene sets | Rice Cis Element Search Tool (RiCES) | Public use website, developed by Koji Doi (NIAS) |
ILRI Programs (Pending)