Software

micca

micca (MICrobial Community Analysis) is a software pipeline for the processing of amplicon sequencing data, from raw sequences to OTU tablestaxonomy classification and phylogenetic tree inference. The pipeline can be applied to a range of highly conserved genes/spacers, such as 16S rRNA geneInternal Transcribed Spacer (ITS) and 28S rRNA.

COLOMBOS

Colombos is a web based portal for exploring and analyzing comprehensive organism-specific cross-platform expression compendia of bacterial organisms. The colombos compendia were carefully constructed by collecting, homogenizing and formally annotating publicly available microarray and RNA-seq experiments from Gene Expression Omnibus (GEO), and ArrayExpress.

VESPUCCI

VESPUCCI is a COLOMBOS technology-based web portal for exploring and analyzing a comprehensive Vitis vinifera specific cross-platform expression compendium. This compendium was carefully constructed by collecting, homogenizing and formally annotating publicly available microarray and RNA-seq experiments from Gene Expression Omnibus (GEO), and ArrayExpress.

PhyloRelief

PhyloRelief implements an algorithm that introduces the Relief strategy of feature weighting in a phylogenetic context to identify those OTUs or groups of OTUs that are correlated for the differentiation between classes of samples (i.e. healthy vs. disease, lean vs. obese etc.) in a metagenomic dataset. 

StrainEst

StrainEst is a novel, reference-based method that uses the Single Nucleotide Variants (SNV) profiles of the available genomes of selected species to determine the number and identity of coexisting strains and their relative abundances in mixed metagenomic samples.

minepy

minepy provides an ANSI C library for the Maximal Information-based Nonparametric Exploration (MIC and MINE family). It includes efficient Python (Python 2 and 3) and MATLAB/Octave APIs and the new MICe and TICe estimators.

MICtools

MICtools is an open source pipeline which combines the TICe and MICe measures into a two-step procedure that allows to identify relationships of various degrees of complexity in large datasets.

ASSIsT

ASSIsT is a user-friendly, customizable pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays. The software is implemented in python and comes with an easy installation package for Windows and Linux.