| Version | MAJ | arb | ||
| none | 2003-08-22 | Download | Doc |
The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria.
Remarque
| Run Unix # arb | Run Web # |
| Version | MAJ | dotur | ||
| 1.53 | 2007-08-30 | Download | Doc |
DOTUR est un programme qui prend en entrée une matrice décrivant les distances génétiques entre des séquences d'ADN pour les assigner à des unités taxonomiques opérationelles (OTUs). DOTUR utilise la composition des OTUs pour calculer des courbes de raréfaction et de collection pour évaluer l'intensité, la richesse et la diversité de l'échantillon.
Remarque
| Run Unix # dotur | Run Web # |
| Version | MAJ | esprit | ||
| 2009-07-07 | Download | Doc |
ESPRIT is a pipeline for estimating species richness using large collections of 16S rRNA pyrosequences.
Remarque
| Run Unix # esprit_pc | Run Web # |
| Version | MAJ | kaiju | ||
| 1.5.0 | 2017-05-14 | Download | Doc |
Kaiju is a program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein sequences.
Remarque Citation Menzel P., Ng K.L., Krogh A. (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7:11257
| Run Unix # kaiju -t nodes.dmp -f kaiju_db.fmi -i reads.fastq [-j reads2.fastq] | Run Web # |
| Version | MAJ | rdp_classifier | ||
| 2.2 | 2014-08-02 | Download | Doc |
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy.
Remarque Exemple : classifier testQuerySeq.fasta mon_result train052008/rRNAClassifier.properties ---Il faut préalablement avoir dans son home le repertoire train052008 http://downloads.sourceforge.net/rdp-classifier/RDPClassifier_train052008.tar.gz) (http://rdp.cme.msu.edu/tmp_download/train3.tar.gz)
| Run Unix # classifier | Run Web # |
