| Metagenomics tools |
website |
| General Software package |
| STAMP |
http://kiwi.cs.dal.ca/Software/STAMP |
| CD-HIT-OUT |
http://weizhong-lab.ucsd.edu/cd-hit-otu/ |
| GAAS |
http://sourceforge.net/projects/gaas/ |
| Megan |
http://www-ab.informatik.unituebingen.de/software/megan/ welcome.html |
| MetaPhlAn |
http://huttenhower.sph.harvard.edu/metaphlan |
| MetaSim |
http://www-ab.informatik.uni-tuebingen.de/software/metasim |
| Mocat |
http://vm-lux.embl.de/~kultima/MOCAT/index.htm |
| Livermore Metagenomics Analysis Toolkit |
https://computation-rnd.llnl.gov/lmat |
| Straine |
http://www.hsls.pitt.edu/obrc/index.php?page=URL1221230034 |
| Metagenome assembly |
|
| Velvet |
http://www.ebi.ac.uk/~zerbino/velvet/ |
| Celera |
http://www.cbcb.umd.edu/research/assembly.shtml#software |
| Metasim |
http://ab.inf.uni-tuebingen.de/software/metasim/welcome.html #Download |
| Euler |
http://nbcr.sdsc.edu/euler/ JAZZ |
| Mapping to reference genome |
| Bowtie |
http://bowtie-bio.sourceforge.net/index.shtml |
| BWA |
http://bio-bwa.sourceforge.net/ |
| MAPLE: |
http://www.genome.jp/maple-bin/mapleSubmit.cgi?aType=sDirect |
| Quality analysis |
|
| FastQC |
http://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc |
| Prinseq |
http://edwards.sdsu.edu/cgi-bin/prinseq/prinseq.cgi |
| Gene calling |
| Genemark. |
hmm http://exon.gatech.edu/GeneMark/metagenome/Prediction/ |
| Microbial diversity Analysis |
| MLST |
http://www. mlst.net) http://www.mlst.net/ |
| MOTHUR |
http://www.mothur.org/ |
| EstimateS |
http://viceroy.eeb.uconn.edu/EstimateS/ |
| QIIME |
http://qiime.org/install/virtual_box.html |
| PHACCS |
http://phaccs.sourceforge.net/ |
| Binning |
|
| TETRA |
http://www.megx.net/tetra/index.html |
| Phylopathia |
http://cbcsrv.watson.ibm.com/phylopythia.html |
| MEGAN |
http://ab.inf.uni-tuebingen.de/software/megan/ |
| CARMA |
http://www.cebitec.uni-bielefeld.de/brf/carma/carma.html |
| Phymm |
http://www.cbcb.umd.edu/software/phymm/ |
| Functional Annotation |
| MEX (Motif Extraction) |
http://adios.tau.ac.il/SPMatch/ |
| RAMMCAP |
http://weizhong-lab.ucsd.edu/rammcap/cgi-bin/rammcap.cgi |
| Analysis of quantitative metagenomics data. |
| FANTOM: |
http://www.sysbio.se/Fantom/ |
| Comparitive Metagenomics |
| MEGAN |
http://metagenomics.anl.gov/ |
| MG-RAST |
http://metagenomics.anl.gov |
| Camera |
http://camera.calit2.net/ |
| Shotgun FunctionalizeR |
http://shotgun.math.chalmers.se/ |
| MetaStats |
http://metastats.cbcb.umd.edu/detection.html |
| UniFrac |
http://bmf.colorado.edu/unifrac/ |
| Galaxy |
https://main.g2.bx.psu.edu/u/aun1/w/metagenomic-analysis |
| MetaMine |
http://www.megx.net/metamine/ |
| MetaLook |
http://www.megx.net/metalook/index.php |
| IMG/M |
http://img.jgi.doe.gov/cgi-bin/m/main.cgi |
| Online tools for NGS analysis |
| Parallel Meta |
http://www.computationalbioenergy.org/parallel-meta.html |
| SOrt-ITEMS |
http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS/ |
| PANGEA |
http://www.ohloh.net/p/pangea-plus |
| Genohub: |
https://genohub.com/bioinformatics/17/metagenomic-analysis |
| Additional Metagenome analysis links |
| EBI Metagenomics: |
https://www.ebi.ac.uk/metagenomics |
| MetaPhlAn: |
http://huttenhower.sph.harvard.edu/metaphlan |
| Amphora |
Net http://pitgroup.org/amphoranet |
