- Tools can be used both on the Mobyle portal or on the local server.
- Tools can be used only on the local server (unix command line).
The latest program's installation from the last 6 months at Institut Pasteur.
2013/04/26
-
crac [more]
Description: a tool to analyze High Throughput Sequencing (HTS)), data in comparison to a reference genome
Version: 1.2.0
Home: http://www.lirmm.fr/~rivals/
-
crac:
-
crac-client:
-
crac-index:
installed version 1.2.0
-
2013/04/16
-
flexbar
Installed version 2.33
-
2013/03/27
-
blast2taxonomy [more]
updated to version 2.1: add krona representation option
-
2013/03/24
-
phyml [more]
Description: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
Version: 20130219.patch
Home: http://code.google.com/p/phyml
-
phyml:
installation version 20120412 patch 20130219
-
2013/03/15
-
t_coffee [more]
Description: A multiple sequence alignment package
Version: 9.03.r1318
Home: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
-
t_coffee:
Installed version 9.03.r1318
taxoptimiser [more]
Description: Taxonomy tools to analyse BLAST Hits.
Version: 1.1
-
rankoptimizer: Taxonomic abundance, based on BLAST hits.
-
kronaextract: Tools to split krona output information.
-
mappinghsp4taxo: Plot tools for rankoptimiser programs.
-
taxoptimizer: Find taxonomy for BLAST hits. Taxonomy information came from NCBI Taxonomy database or from the public sequence databases.
updated to version 1.1: rankoptimizer: new option: Report lowest common ancestor of tree
-
2013/03/14
-
fqtools [more]
Description: FastQ sequences files utilities
Version: 1.0a
-
fqquality: FastQ sequences quality filter
-
fqextract: FastQ sequences extractor
-
fqconvert: convert quality scoring to Sanger in FASTQ files
-
fqduplicate: FastQ sequences duplicate finder
Updated from developpement version
-
2013/03/13
-
taxoptimiser [more]
Description: Taxonomy tools to analyse BLAST Hits.
Version: 1.1
-
rankoptimizer: Taxonomic abundance, based on BLAST hits.
-
kronaextract: Tools to split krona output information.
-
mappinghsp4taxo: Plot tools for rankoptimiser programs.
-
taxoptimizer: Find taxonomy for BLAST hits. Taxonomy information came from NCBI Taxonomy database or from the public sequence databases.
rankoptimizer: fix krona-2.0 javascript problem
-
2013/03/12
-
fqtools [more]
Description: FastQ sequences files utilities
Version: 1.0a
-
fqquality: FastQ sequences quality filter
-
fqextract: FastQ sequences extractor
-
fqconvert: convert quality scoring to Sanger in FASTQ files
-
fqduplicate: FastQ sequences duplicate finder
Updated from developpement version
-
2013/03/05
-
fqtools [more]
Description: FastQ sequences files utilities
Version: 1.0a
-
fqquality: FastQ sequences quality filter
-
fqextract: FastQ sequences extractor
-
fqconvert: convert quality scoring to Sanger in FASTQ files
-
fqduplicate: FastQ sequences duplicate finder
Updated from developpement version
-
2013/03/04
-
fqtools [more]
Description: FastQ sequences files utilities
Version: 1.0a
-
fqquality: FastQ sequences quality filter
-
fqextract: FastQ sequences extractor
-
fqconvert: convert quality scoring to Sanger in FASTQ files
-
fqduplicate: FastQ sequences duplicate finder
Updated from developpement version
-
2013/02/28
-
taxoptimiser [more]
Description: Taxonomy tools to analyse BLAST Hits.
Version: 1.1
-
rankoptimizer: Taxonomic abundance, based on BLAST hits.
-
kronaextract: Tools to split krona output information.
-
mappinghsp4taxo: Plot tools for rankoptimiser programs.
-
taxoptimizer: Find taxonomy for BLAST hits. Taxonomy information came from NCBI Taxonomy database or from the public sequence databases.
taxoptimizer: new supported taxonomy databases (rdpii, silva ann greengenes taxonomy)
-
2013/02/27
-
fatools [more]
Description: FASTA sequences files utilities
Version: 0.99
-
famerge: Merge fasta entries with the same sequence
First installation from developpement version
-
2013/02/25
-
fqtools [more]
Description: FastQ sequences files utilities
Version: 1.0a
-
fqquality: FastQ sequences quality filter
-
fqextract: FastQ sequences extractor
-
fqconvert: convert quality scoring to Sanger in FASTQ files
-
fqduplicate: FastQ sequences duplicate finder
Updated from developpement version
-
2013/02/21
-
taxodb [more]
Description: Create Barkeley database for taxonomy of 16S databases
Version: 1.0
-
taxodbfa.py: Create Barkeley database for taxonomy of 16S databases in fasta format.
installation version 1.0
-
2013/02/19
-
ptools [more]
Description: Parallel versions of various tools
Version: 0.99
-
pbwa: Burrows-Wheeler Alignment tool, parallel version
-
pfqextract: Extract entries by name from FASTQ formatted files, parallel version
-
pcmsearch: Search a sequence database for RNAs homologous to a CM, parallel version
-
pblastall: Comparison between two sequences with Blast (NCBI), parallel version
-
ptaxoptimizer: Find taxonomy for BLAST hits, parallel version
-
pmaq: Mapping and Assembly with Qualities, parallel version
Updated from developpement version
-
2013/02/14
-
fqtools [more]
Description: FastQ sequences files utilities
Version: 1.0a
-
fqquality: FastQ sequences quality filter
-
fqextract: FastQ sequences extractor
-
fqconvert: convert quality scoring to Sanger in FASTQ files
-
fqduplicate: FastQ sequences duplicate finder
Updated from developpement version
-
2013/02/13
-
dash [more]
Description: DASH (DASH Associates Shared Haplotypes), that builds upon pairwise IBD shared segments to infer clusters of IBD individuals
Version: 1.1.0
Home: http://www1.cs.columbia.edu/~gusev/dash/
-
bgl_to_ped:
-
dash_adv:
-
dash_cc:
-
dash_cc.sh:
-
gline.for_dash.sh:
-
gline.sh:
-
hom_to_ped:
-
ped_to_bgl:
-
ped_to_hom:
-
phase.sh:
-
search:
Installed version 1.1.0
germline [more]
Description: GERMLINE is an algorithm for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population
Version: 1.5.1
Home: http://www1.cs.columbia.edu/~gusev/germline/
-
germline:
Installed version 1.5.1
biofilter [more]
Description: a software tool that provides a convenient single interface for accessing multiple publicly available human genetic data sources.
Version: 2.0.0rc2
Home: http://ritchielab.psu.edu/ritchielab/software/
-
biofilter.py:
-
buildPopulations.py:
-
loki-build.py:
Installed version 2.0.0rc2
beagle [more]
Description: a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples.
Version: 3.3.2
Home: http://faculty.washington.edu/browning/beagle/beagle.html
Installed version 3.3.2
emmax [more]
Description: statistical test for large scale human or model organism association mapping accounting for the sample structure
Version: beta-07Mar2010
Home: http://genetics.cs.ucla.edu/emmax/index.html
-
emmax:
-
emmax-kin:
Installed version beta-07Mar2010
-
2013/02/08
-
fqtools [more]
Description: FastQ sequences files utilities
Version: 1.0a
-
fqquality: FastQ sequences quality filter
-
fqextract: FastQ sequences extractor
-
fqconvert: convert quality scoring to Sanger in FASTQ files
-
fqduplicate: FastQ sequences duplicate finder
Updated from developpement version
squizz [more]
Description: Sequence/Alignment format checker
Version: 0.99b
-
squizz_checker: Sequence/Alignment format checker
squizz_convert: Sequence/Alignment format checker
squizz: Sequence/Alignment format checker
Updated from developpement version
-
2013/02/07
-
squizz [more]
Description: Sequence/Alignment format checker
Version: 0.99b
-
squizz_checker: Sequence/Alignment format checker
squizz_convert: Sequence/Alignment format checker
squizz: Sequence/Alignment format checker
Updated from developpement version
-
2013/02/05
-
Clustal-Omega [more]
Description: CLUSTAL-OMEGA is a general purpose multiple sequence alignment program.
Version: 1.1.0
Home: http://www.clustal.org/
-
clustalo:
upgrade to version 1.1.0 (support of DNA/RNA)
-
2013/01/30
-
crop [more]
Description: clustering tool designed mainly for Metagenomics studies, which clusters 16S rRNA sequences into Operational Taxonomic Units
Version: v1.33
Home: http://code.google.com/p/crop-tingchenlab/
-
CROPLinux:
installed v1.33
GemSIM [more]
Description: software package for generating realistic simulated next-generation sequencing reads with quality score values
Version: v1.6
Home: http://gemsim.sourceforge.net/
-
GemErr.py:
-
GemHaps.py:
-
GemReads.py:
-
GemStats.py:
installed v1.6
cd-hit [more]
Description: a program for clustering DNA/protein sequence database at high identity with tolerance.
Version: v4.6.1
Home: https://code.google.com/p/cdhit/
-
cd-hit:
-
cd-hit-2d:
-
cd-hit-2d-para.pl:
-
cd-hit-454:
-
cd-hit-div:
-
cd-hit-div.pl:
-
cd-hit-est:
-
cd-hit-est-2d:
-
cd-hit-para.pl:
-
clstr2tree.pl:
-
clstr2txt.pl:
-
clstr2xml.pl:
-
clstr_cut.pl:
-
clstr_merge.pl:
-
clstr_merge_noorder.pl:
-
clstr_quality_eval.pl:
-
clstr_quality_eval_by_link.pl:
-
clstr_reduce.pl:
-
clstr_renumber.pl:
-
clstr_rep.pl:
-
clstr_reps_faa_rev.pl:
-
clstr_rev.pl:
-
clstr_select.pl:
-
clstr_select_rep.pl:
-
clstr_size_histogram.pl:
-
clstr_size_stat.pl:
-
clstr_sort_by.pl:
-
clstr_sort_prot_by.pl:
-
clstr_sql_tbl.pl:
-
clstr_sql_tbl_sort.pl:
-
make_multi_seq.pl:
-
plot_2d.pl:
-
plot_len1.pl:
-
psi-cd-hit-2d-g1.pl:
-
psi-cd-hit-2d.pl:
-
psi-cd-hit-local.pl:
-
psi-cd-hit.pl:
installed v4.6.1
-
2013/01/25
-
ptools [more]
Description: Parallel versions of various tools
Version: 0.99
-
pbwa: Burrows-Wheeler Alignment tool, parallel version
-
pfqextract: Extract entries by name from FASTQ formatted files, parallel version
-
pcmsearch: Search a sequence database for RNAs homologous to a CM, parallel version
-
pblastall: Comparison between two sequences with Blast (NCBI), parallel version
-
ptaxoptimizer: Find taxonomy for BLAST hits, parallel version
-
pmaq: Mapping and Assembly with Qualities, parallel version
Updated from developpement version
-
2013/01/21
-
squizz [more]
Description: Sequence/Alignment format checker
Version: 0.99b
-
squizz_checker: Sequence/Alignment format checker
squizz_convert: Sequence/Alignment format checker
squizz: Sequence/Alignment format checker
Updated from developpement version
taxoptimiser [more]
Description: Taxonomy tools to analyse BLAST Hits.
Version: 1.1
-
rankoptimizer: Taxonomic abundance, based on BLAST hits.
-
kronaextract: Tools to split krona output information.
-
mappinghsp4taxo: Plot tools for rankoptimiser programs.
-
taxoptimizer: Find taxonomy for BLAST hits. Taxonomy information came from NCBI Taxonomy database or from the public sequence databases.
rankoptimizer: bug fix
-
2013/01/18
-
ptools [more]
Description: Parallel versions of various tools
Version: 0.99
-
pbwa: Burrows-Wheeler Alignment tool, parallel version
-
pfqextract: Extract entries by name from FASTQ formatted files, parallel version
-
pcmsearch: Search a sequence database for RNAs homologous to a CM, parallel version
-
pblastall: Comparison between two sequences with Blast (NCBI), parallel version
-
ptaxoptimizer: Find taxonomy for BLAST hits, parallel version
-
pmaq: Mapping and Assembly with Qualities, parallel version
Updated from developpement version
-
2013/01/10
-
ptools [more]
Description: Parallel versions of various tools
Version: 0.99
-
pbwa: Burrows-Wheeler Alignment tool, parallel version
-
pfqextract: Extract entries by name from FASTQ formatted files, parallel version
-
pcmsearch: Search a sequence database for RNAs homologous to a CM, parallel version
-
pblastall: Comparison between two sequences with Blast (NCBI), parallel version
-
ptaxoptimizer: Find taxonomy for BLAST hits, parallel version
-
pmaq: Mapping and Assembly with Qualities, parallel version
Updated from developpement version
-
2013/01/09
-
ptools [more]
Description: Parallel versions of various tools
Version: 0.99
-
pbwa: Burrows-Wheeler Alignment tool, parallel version
-
pfqextract: Extract entries by name from FASTQ formatted files, parallel version
-
pcmsearch: Search a sequence database for RNAs homologous to a CM, parallel version
-
pblastall: Comparison between two sequences with Blast (NCBI), parallel version
-
ptaxoptimizer: Find taxonomy for BLAST hits, parallel version
-
pmaq: Mapping and Assembly with Qualities, parallel version
Updated from developpement version
-
2013/01/08
-
squizz [more]
Description: Sequence/Alignment format checker
Version: 0.99b
-
squizz_checker: Sequence/Alignment format checker
squizz_convert: Sequence/Alignment format checker
squizz: Sequence/Alignment format checker
Updated from developpement version
taxoptimiser [more]
Description: Taxonomy tools to analyse BLAST Hits.
Version: 1.1
-
rankoptimizer: Taxonomic abundance, based on BLAST hits.
-
kronaextract: Tools to split krona output information.
-
mappinghsp4taxo: Plot tools for rankoptimiser programs.
-
taxoptimizer: Find taxonomy for BLAST hits. Taxonomy information came from NCBI Taxonomy database or from the public sequence databases.
kronaextract: extract list of reads for on taxonomic name
-
2013/01/07
-
clcgenomicsworkbench [more]
Description: Graphic interface to launch the proprietary NGS data dedicated programs (read trimming, mapping, de novo assembly, SNP calling...)
Version: 5.5.2
Home: http://www.clcbio.com/
-
clcgenomicswb:
updated to version 5.5.2
-
2012/12/28
-
taxoptimiser [more]
Description: Taxonomy tools to analyse BLAST Hits.
Version: 1.1
-
rankoptimizer: Taxonomic abundance, based on BLAST hits.
-
kronaextract: Tools to split krona output information.
-
mappinghsp4taxo: Plot tools for rankoptimiser programs.
-
taxoptimizer: Find taxonomy for BLAST hits. Taxonomy information came from NCBI Taxonomy database or from the public sequence databases.
rankoptimizer: krona javascript incorporated in html output.
-
2012/12/21
-
fastqc [more]
Description: A quality control tool for high throughput sequence data.
Version: 0.10.1
Home: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc
-
fastqc: quality control tool for high throughput sequence data.
Installed version 0.10.1
ECHO [more]
Description: an error correction algorithm designed for short-reads from next-generation sequencing platforms
Version: 1.12
Home: http://uc-echo.sourceforge.net/
-
ErrorCorrection.py:
Installed version 1.12
-
2012/12/14
-
fqtools [more]
Description: FastQ sequences files utilities
Version: 1.0a
-
fqquality: FastQ sequences quality filter
-
fqextract: FastQ sequences extractor
-
fqconvert: convert quality scoring to Sanger in FASTQ files
-
fqduplicate: FastQ sequences duplicate finder
Updated from developpement version
-
2012/12/11
-
freec [more]
Description: a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data
Version: 6.3
Home: http://bioinfo.curie.fr/projects/freec
-
freec:
Installed v5.8
seqtools [more]
Description: A suite of tools for visualising sequence alignments
Version: 4.17
Home: http://www.sanger.ac.uk/resources/software/seqtools/
-
dotter: graphical dot-matrix program for detailed comparison of two sequences
-
blixem: interactive browser of pairwise alignments
-
belvu: multiple sequence alignment viewer and phylogenetic tool
installed version 4.17
dotter
removed. superseeded by seqtools suite.
-
2012/12/04
-
snpEff [more]
Description: It's a variant effect predictor tool, it predicts the effect of genetic variations (SNPs, insertions, deletions and MNPs)
Version: 3.0
Home: http://snpeff.sourceforge.net/
-
snpEff: Variant effect predictor tool
Installed version 3.1h
-
2012/12/03
-
ptools [more]
Description: Parallel versions of various tools
Version: 0.99
-
pbwa: Burrows-Wheeler Alignment tool, parallel version
-
pfqextract: Extract entries by name from FASTQ formatted files, parallel version
-
pcmsearch: Search a sequence database for RNAs homologous to a CM, parallel version
-
pblastall: Comparison between two sequences with Blast (NCBI), parallel version
-
ptaxoptimizer: Find taxonomy for BLAST hits, parallel version
-
pmaq: Mapping and Assembly with Qualities, parallel version
Updated from developpement version
-
2012/11/16
-
html4blast [more]
Description: A simple Text to HTML blast results formatter
Version: 1.7a
-
html4blast: HTML blast results formatter
html4blast: HTML blast results formatter
Updated from developpement version
-
2012/11/14
-
penncnv [more]
Description: CNV detection from Illumina whole-genome SNP genotyping arrays. It has been extended to handle candidate gene SNP arrays, to handle recent high-density arrays with non-polymorphic markers (so-called CN markers), and to handle Affymetrix genome-wide arrays
Version: 2009.08.27
Home: http://www.openbioinformatics.org/penncnv/
-
cal_gc_snp.pl: Calculate GC content surrounding each marker within specified sliding window, using the UCSC GC annotation file that is also sorted
-
genomic_wave.pl: Calculate or adjust for genomic waves in signal intensities for whole-genome SNP genotyping arrays
-
compile_pfb.pl: Compile PFB file from multiple signal intensity files containing BAF values
-
convert_cnv.pl: Convert formats between CNV calls generated from different programs/algorithms
-
detect_cnv: Generate CNV calls from high-density SNP genotyping data that contains Log R Ratio and B Allele Frequency for each SNP or CN marker
detect_cnv.pl: Generate CNV calls from high-density SNP genotyping data that contains Log R Ratio and B Allele Frequency for each SNP or CN marker
-
infer_snp_allele.pl: Infer SNP genotypes in CNV regions, or assign P-values to putative de-novo CNV calls
-
detect_cnv: Perform column extraction operations
kcolumn.pl: Perform column extraction operations
-
compare_cnv.pl: Perform comparative analysis of CNV calls
-
detect_cnv: Reformat CNV calls by PennCNV for visualization in UCSC Genome Browser, in web browser, or in BeadStudio software
visualize_cnv.pl: Reformat CNV calls by PennCNV for visualization in UCSC Genome Browser, in web browser, or in BeadStudio software
-
scan_region: Scan genomic regions in a query-file against a DB-file which contains chromosome locations for various genomics features
scan_region.pl: Scan genomic regions in a query-file against a DB-file which contains chromosome locations for various genomics features
-
split_illumina_report.pl: Split the Illumina report file to individual signal intensity files
-
filter_cnv.pl: filter CNV calls from input by various criteria
-
clean_cnv.pl: post-process CNV calls
Updated to lastest version (20121114)
-
2012/11/06
-
ptools [more]
Description: Parallel versions of various tools
Version: 0.99
-
pbwa: Burrows-Wheeler Alignment tool, parallel version
-
pfqextract: Extract entries by name from FASTQ formatted files, parallel version
-
pcmsearch: Search a sequence database for RNAs homologous to a CM, parallel version
-
pblastall: Comparison between two sequences with Blast (NCBI), parallel version
-
ptaxoptimizer: Find taxonomy for BLAST hits, parallel version
-
pmaq: Mapping and Assembly with Qualities, parallel version
Updated from developpement version
-
2012/10/31
-
ptools [more]
Description: Parallel versions of various tools
Version: 0.99
-
pbwa: Burrows-Wheeler Alignment tool, parallel version
-
pfqextract: Extract entries by name from FASTQ formatted files, parallel version
-
pcmsearch: Search a sequence database for RNAs homologous to a CM, parallel version
-
pblastall: Comparison between two sequences with Blast (NCBI), parallel version
-
ptaxoptimizer: Find taxonomy for BLAST hits, parallel version
-
pmaq: Mapping and Assembly with Qualities, parallel version
Updated from developpement version
-