Les deux révisions précédentesRévision précédenteProchaine révision | Révision précédente |
documentation:tools:software:bioinfo [2018/03/26 12:48] – cpetit | documentation:tools:software:bioinfo [2020/10/05 09:37] (Version actuelle) – [Logiciels Bioinformatiques] ltaulell |
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<WRAP col3> | <WRAP col3> |
* Alignment | * Alignment |
* [[documentation:tools:software:blat|BLAT]] | * [[documentation:tools:software:blat|BLAT]] |
* [[documentation:tools:software:blast|NCBI BLAST2 / BLAST+]] | * [[documentation:tools:software:blast|NCBI BLAST2 / BLAST+]] |
* [[documentation:tools:software:bowtie|Bowtie]] | * [[documentation:tools:software:bowtie|Bowtie]] |
* [[documentation:tools:software:bwakit|BWA]] (Bwakit) | * [[documentation:tools:software:bwakit|BWA]] (Bwakit) |
* [[documentation:tools:software:clustalomega|ClustalOmega]] | * [[documentation:tools:software:clustalomega|ClustalOmega]] |
* [[documentation:tools:software:exonerate|Exonerate]] | * [[documentation:tools:software:exonerate|Exonerate]] |
* [[documentation:tools:software:gblocks|Gblocks]] | * [[documentation:tools:software:gblocks|Gblocks]] |
* [[documentation:tools:software:gmap-gsnap|GMAP/GSNAP]] | * [[documentation:tools:software:gmap-gsnap|GMAP/GSNAP]] |
* [[documentation:tools:software:mafft|MAFFT]] | * [[documentation:tools:software:mafft|MAFFT]] |
* [[documentation:tools:software:prank|Prank]] | * [[documentation:tools:software:prank|Prank]] |
* [[documentation:tools:software:seaview|SeaView]] | * [[documentation:tools:software:seaview|SeaView]] |
* [[documentation:tools:software:snap|SNAP]] | * [[documentation:tools:software:snap|SNAP]] |
* [[documentation:tools:software:star|STAR]] | * [[documentation:tools:software:star|STAR]] |
* [[documentation:tools:software:tcoffee|T-Coffee]] | * [[documentation:tools:software:tcoffee|T-Coffee]] |
* [[documentation:tools:software:hmmer|HMMER /HMMER2]] | * [[documentation:tools:software:hmmer|HMMER /HMMER2]] |
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* Genome Assembly | * Genome Assembly |
* [[documentation:tools:software:velvet|Velvet]] | * [[documentation:tools:software:velvet|Velvet]] |
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* Transciptomes Assembly | * Transcriptomes Assembly |
* [[documentation:tools:software:cufflinks|Cufflinks]] | * [[documentation:tools:software:cufflinks|Cufflinks]] |
* [[documentation:tools:software:hisat|HISAT]] | * [[documentation:tools:software:hisat|HISAT]] |
* <del> MaLTA </del> [[http://alan.cs.gsu.edu/NGS/?q=malta|.]] | * <del> MaLTA </del> [[http://alan.cs.gsu.edu/NGS/?q=malta|.]] |
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* //de novo// assembly | * //de novo// assembly |
* [[documentation:tools:software:atram|aTRAM]] | * <del>|aTRAM</del> |
* [[documentation:tools:software:apytram|apytram]] | * <del>apytram</del> |
* [[documentation:tools:software:bridger|Bridger]] | * <del>Bridger</del> |
* [[documentation:tools:software:canu|Canu]] | * [[documentation:tools:software:canu|Canu]] |
* [[documentation:tools:software:celera-wgs|Celera-WGS]] | * <del>Celera-WGS</del> |
* [[documentation:tools:software:corset|Corset]] | * [[documentation:tools:software:corset|Corset]] |
* [[documentation:tools:software:mira|MIRA]] | * [[documentation:tools:software:mira|MIRA]] |
* [[documentation:tools:software:oases|Oases]] | * <del>Oases</del> |
* [[documentation:tools:software:stringtie|StringTie]] | * [[documentation:tools:software:stringtie|StringTie]] |
* [[documentation:tools:software:trinity|Trinity]] | * [[documentation:tools:software:trinity|Trinity]] |
* [[documentation:tools:software:velvet|Velvet]] | * [[documentation:tools:software:velvet|Velvet]] |
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* Genome/Transcriptome Annotation | * Genome/Transcriptome Annotation |
* [[documentation:tools:software:braker|Braker]] | * [[documentation:tools:software:braker|Braker]] |
* [[documentation:tools:software:genemark|GeneMark ES/ET]] | * [[documentation:tools:software:genemark|GeneMark ES/ET]] |
* [[documentation:tools:software:phylomerge|PhyloMerge]] | |
* [[documentation:tools:software:transdecoder|TransDecoder]] | * [[documentation:tools:software:transdecoder|TransDecoder]] |
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* Sequences clustering | * Sequences clustering |
* [[documentation:tools:software:amalgam|amalgam]] | * <del>SiLiX</del> |
* [[documentation:tools:software:silix|SiLiX]] | |
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* Estimate RNA-seq Abundance | * Estimate RNA-seq Abundance |
* [[documentation:tools:software:cufflinks|Cufflinks]] | * [[documentation:tools:software:cufflinks|Cufflinks]] |
* [[documentation:tools:software:stringtie|StringTie]] | * [[documentation:tools:software:stringtie|StringTie]] |
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* SNP | * SNP |
* [[documentation:tools:software:bcftools|BCFtools]] | * [[documentation:tools:software:bcftools|BCFtools]] |
* [[documentation:tools:software:breseq|breseq]] | * [[documentation:tools:software:breseq|breseq]] |
* [[documentation:tools:software:discosnp|DiscoSNP]] | * [[documentation:tools:software:discosnp|DiscoSNP]] |
* [[documentation:tools:software:gatk|GATK]] | * [[documentation:tools:software:gatk|GATK]] |
* [[documentation:tools:software:kissplice|KisSplice]] | * [[documentation:tools:software:kissplice|KisSplice]] |
* [[documentation:tools:software:snpeff|SnpEff]] | * [[documentation:tools:software:snpeff|SnpEff]] |
* <del> SNPScanner </del> | * <del> SNPScanner </del> |
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* Phylogeny | * Phylogeny |
* [[documentation:tools:software:amalgam|caars]] | |
* [[documentation:tools:software:fasttree|FastTree]] | * [[documentation:tools:software:fasttree|FastTree]] |
* [[documentation:tools:software:gubbins|Gubbins]] | * [[documentation:tools:software:gubbins|Gubbins]] |
* [[documentation:tools:software:hyphy|HyPhy]] | * [[documentation:tools:software:hyphy|HyPhy]] |
* [[documentation:tools:software:mrbayes|MRbayes]] | * [[documentation:tools:software:mrbayes|MRbayes]] |
* [[documentation:tools:software:phyldog|PHYLDOG]] | * <del>PHYLDOG</del> |
* [[documentation:tools:software:phylobayes|Phylobayes]] | |
* [[documentation:tools:software:phylomerge|PhyloMerge]] | |
* [[documentation:tools:software:phyml|PhyML]] | * [[documentation:tools:software:phyml|PhyML]] |
* [[documentation:tools:software:raxml|RAxML]] | * [[documentation:tools:software:raxml|RAxML]] |
* <del> Guidance & Guidance2 </del> | * <del> Guidance & Guidance2 </del> |
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* ChIP-seq Analysis | * ChIP-seq Analysis |
* [[documentation:tools:software:drompa|DROMPA]] | * [[documentation:tools:software:drompa|DROMPA]] |
* [[documentation:tools:software:macs|MACS/MACS2]] | * [[documentation:tools:software:macs|MACS/MACS2]] |
* [[documentation:tools:software:music|MUSIC]] | * [[documentation:tools:software:music|MUSIC]] |
* [[documentation:tools:software:odin|ODIN (RGT)]] | * [[documentation:tools:software:odin|ODIN]] |
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* Nucleosomes Mapping | * Nucleosomes Mapping |
* [[documentation:tools:software:nucleominer|NucleoMiner]] | * <del>NucleoMiner</del> |
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* Handle NGS Data | * Handle NGS Data |
* [[documentation:tools:software:bamtools|BamTools]] | * [[documentation:tools:software:bamtools|BamTools]] |
* [[documentation:tools:software:bedtools|BEDTools]] | * [[documentation:tools:software:bedtools|BEDTools]] |
* [[documentation:tools:software:fastq-tools|fastq-tools]] | * [[documentation:tools:software:fastq-tools|fastq-tools]] |
* [[documentation:tools:software:fastx-toolkit|FASTX-Toolkit]] | * [[documentation:tools:software:fastx-toolkit|FASTX-Toolkit]] |
* [[documentation:tools:software:htseq|HTSeq]] | * [[documentation:tools:software:htseq|HTSeq]] |
* [[documentation:tools:software:htslib|HTSlib]]/[[documentation:tools:software:bcftools|bcftools]]/[[documentation:tools:software:samtools|SAMtools]] | * [[documentation:tools:software:htslib|HTSlib]]/[[documentation:tools:software:bcftools|bcftools]]/[[documentation:tools:software:samtools|SAMtools]] |
* [[documentation:tools:software:picard|Picard]] | * [[documentation:tools:software:picard|Picard]] |
* [[documentation:tools:software:sratoolkit|SRAToolkit]] | * [[documentation:tools:software:sratoolkit|SRAToolkit]] |
* [[documentation:tools:software:tablemaker|tablemaker]] | * [[documentation:tools:software:tablemaker|tablemaker]] |
* [[documentation:tools:software:jellyfish|Jellyfish]] | * [[documentation:tools:software:jellyfish|Jellyfish]] |
* <del> Homer </del> [[http://homer.ucsd.edu/homer/|.]] | * <del>Homer</del> |
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* NGS data visualization | |
* [[documentation:tools:software:pybigwig|pyBigWig]] | |
* [[documentation:tools:software:ucsc|UCSC]] | |
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| * NGS data visualization |
| * [[documentation:tools:software:pybigwig|pyBigWig]] |
| * [[documentation:tools:software:ucsc|UCSC]] |
* Trim rna-seq reads | * Trim rna-seq reads |
* [[documentation:tools:software:prinseq-lite|prinseq-lite]] | * [[documentation:tools:software:prinseq-lite|prinseq-lite]] |
* [[documentation:tools:software:trimmomatic|Trimmomatic]] | * [[documentation:tools:software:trimmomatic|Trimmomatic]] |
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* Libraries /Languages | * Libraries /Languages |
* [[documentation:tools:software:biopython|Biopython]] | * [[documentation:tools:software:biopython|Biopython]] |
* [[documentation:tools:software:seqan|SeqAn]] | * [[documentation:tools:software:seqan|SeqAn]] |
* [[documentation:tools:langages:perl5|Perl5]] <del> BioPerl </del> | * [[documentation:tools:langages:perl5|Perl5]] <del> BioPerl </del> |
* [[documentation:tools:software:r|R]] | * [[documentation:tools:software:r|R]] |
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* NGS suites | * NGS suites |
* [[documentation:tools:software:meme|MEME Suite]] | * [[documentation:tools:software:meme|MEME Suite]] |
* [[documentation:tools:software:novocraft|NovoCraft]] | * [[documentation:tools:software:novocraft|NovoCraft]] |
* [[documentation:tools:software:trinotate|Trinotate]] | * [[documentation:tools:software:trinotate|Trinotate]] |
* [[documentation:tools:software:ucsc|UCSC]] | * [[documentation:tools:software:ucsc|UCSC]] |
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* Quality Control NGS Data | * Quality Control NGS Data |
* [[documentation:tools:software:fastqc|FastQC]] | * [[documentation:tools:software:fastqc|FastQC]] |
* [[documentation:tools:software:rseqc|RSeQC]] | * [[documentation:tools:software:rnaseqc|RNAseq-QC]] |
* [[documentation:tools:software:quast|Quast]] | * [[documentation:tools:software:rseqc|RSeQC]] |
| * [[documentation:tools:software:quast|Quast]] |
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* Bisulfite mapping methylation call | * Bisulfite mapping methylation call |
* [[documentation:tools:software:bismark|Bismark]] | * [[documentation:tools:software:bismark|Bismark]] |
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* Clustering | * Clustering |
* [[documentation:tools:software:cafs|CAFS]] | * [[documentation:tools:software:cafs|CAFS]] |
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* Detection of reconbination | * Detection of reconbination |
* [[documentation:tools:software:clonalframeml|ClonalFrameML]] | * [[documentation:tools:software:clonalframeml|ClonalFrameML]] |
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* DNA methylation | * DNA methylation |
* [[documentation:tools:software:dmap|DMAP]] | * [[documentation:tools:software:dmap|DMAP]] |
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* Tools for Molecular Biology | * Tools for Molecular Biology |
* [[documentation:tools:software:emboss|EMBOSS Suite]] | * [[documentation:tools:software:emboss|EMBOSS Suite]] |
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* PCR Primers | * PCR Primers |
* [[documentation:tools:software:primer3|Primer3]] | * [[documentation:tools:software:primer3|Primer3]] |
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* NMR | * NMR |
* [[documentation:tools:software:spinevolution|Spinevolution]] | * <del>Spinevolution</del> |
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* DNase-seq Analysis | * DNase-seq Analysis |
* [[documentation:tools:software:pydnase|pyDNase]] | * [[documentation:tools:software:pydnase|pyDNase]] |
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* Predict RNA secondary strucures | * Predict RNA secondary strucures |
* [[documentation:tools:software:viennarna|ViennaRNA]] | * [[documentation:tools:software:viennarna|ViennaRNA]] |
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</WRAP> | </WRAP> |