Computational tools for microbiome research
- Subtractive assembly approaches for disease-associated sug-metagenome identification
- ML tools for microbiome-based predictions
- Mi2P: Microbiome to Phenotype
- Tools for metatranscriptomic data analyses
- TAG: assembly of metatranscriptome by mapping transcript sequencing data onto assembly graph of matched metagenome
- Tools for metaproteomics data analyses
- Graph2Pep and Graph2Pro: graph-centric tools for protein identification from MS/MS spectra data of microbial communities
- HAPiID: HAPiID (pronunciation: Happy ID). High Abundance Protein guided Metaproteomics identification
- Gene prediction & assembly & similarity search
- FragGeneScan: a tool for fragmental gene prediction from short reads
- RAPSearch: a fast tool for protein similarity search
- RAPSearch2: an even faster RAPSearch that supports multi-threading.
- GeneStitch: Gene assembly by network matching algorithm
- Inference of pathways and reactions
- MinPath: a parsimony approach for biological pathway reconstructions using protein family predictions
- MetaNetSam: an application for sampling subnetworks from metabolic networks
- PhyloMint: Pathway-based and phylogenetically adjusted quantification of competition and cooperation between microbial species.
- Functional elements minning
- Binning
- AbundanceBin: abundance-based tool for binning metagenomic sequences
- Tools for 16S rRNA sequences analysis
- AbundantOTU (and AbundantOTU+): a tool for fast and accurate identification and quantification of abundant species from pyrosequences of 16S rRNA by using consensus alignment
- PHYLOSHOP: a tool for extracting ribosomal RNA fragments from WGS and simple analysis of ribosomal RNAs
Contact: Yuzhen Ye (yye@indiana.edu) (web)
Currently supported by NIH grant 1R01AI108888; earlier CAREER: 0845685 & NIH grant 01HG004908.
Last modified on July, 2021