| S. No | Software | Platform | Description | Website | References |
|---|---|---|---|---|---|
| 1. | CowPI | Stand alone | A functional inference software used for rumen microbiome analysis. | http://www.cowpi.org | [91] |
| 2. | Microbiome Analyst | Web server | A complete statistical, visual and meta-analysis software for microbiome data analysis. | http://www.microbiomeanalyst.ca/ | [92] |
| 3. | EBI | Web server | To compare functional analyses of sequence. | https://www.ebi.ac.uk/metagenomics/ | [93] |
| 4. | MetaBAT | Web server | Binning millions of contigs from thousands of samples. |
https://bitbucket.org/ berkeleylab/metabat |
[94] |
| 5. | GraPhlAn | Web server | Produces high-quality, compact visualizations of microbial genomes and metagenomes. | http://segatalab.cibio.unitn.it/tools/graphlan | [95] |
| 6. | deFUME | Web server | It is an east to use web server for trimming, assembly and functional annotation of sanger sequencing data derived from functional selection experiments. | http://www.cbs.dtu.dk/services/deFUME/ | [96] |
| 7. | METAVIR | Web server | Annotate viral metagenomics sequences (raw reads assembled contigs). | http://metavir-meb.univbpclermont.fr/ | [97] |
| 8. | VAMPS | Web server | An integrated tool used for data visualization and analysis obtained for microbial population. | https://vamps2.mbl.edu | [98] |
| 9. | MyTaxa | Web server | to identify the taxonomic affiliation of a query genome sequence or a sequence of a contig assembled from a metagenome, including short sequences (e.g., 100-1,000nt long), and to classify sequences representing novel taxa at three levels (whenever possible), i.e., species, genus and phylum. | http://enve-omics.ce.gatech.edu/mytaxa | [99] |
| 10. | Phinch | Web server | It provides an interactive visualization tool that allows users to explore and manipulate large biological datasets. | http://phinch.org/ | [100] |
| 11. | Orione, | Web server | Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology data analysis. | http://orione.crs4.it. | [101] |
| 12. | PICRUSt | Stand alone | A computational approach used for functional profiling of a metagenome using 16S amplicon sequencing. | http://picrust.github.com/ | [102] |
| 13. | FANTOM | Stand alone | Comparative analysis of metagenomics abundance data. | http://www.sysbio.se/Fantom/ | [103] |
| 14. | Meta Microbes Online | Web server | Offers phylogenetic analysis of genes from microbial genomes and metagenomes. | http://meta.MicrobesOnline.org | [104] |
| 15. | METAGENassist | Web server | METAGENassist is a freely available web server for comparative metagenomic analysis. Comparative metagenomic studies involve the large-scale comparison of genomic or taxonomic census data from bacterial samples across different environments. | http://www.metagenassist.ca/METAGENassist/ | [105] |
| 16. | HUMAnN | Stand alone | Analysis of metagenomic shotgun data from the Human Microbiome Project. |
http://huttenhower.sph.harvard.edu/ humann | [106] |
| 17. | MetaPhlAn | Stand alone | Faster profiling of the composition of microbial communities usingunique clade-specific marker genes. | http://huttenhower.sph.harvard.edu/metaphlan | [107] |
| 18. | MetaVelvet | Stand alone | High quality metagenomic assembler | http://metavelvet.dna.bio.keio.ac.jp/ | [108] |
| 19. | SOAPdenovo2 | Stand alone | Metagenomic assembler, specifically for Illumina GA short reads. | http://soap.genomics.org.cn/soapdenovo.html | [109] |
| 20. | WebMGA | Web server | A customizable web server for metagenomic analysis. | http://weizhongli-lab.org/metagenomic-analysis/ | [110] |
| 21. | CoMet | Web server | The CoMet-Universe server allows you to analyze the taxonomic and functional composition of your metagenomic sample and to compare it with a large collection of publicly available data from previous metagenome studies. | http://comet.gobics.de | [111] |
| 22. | MEGAN | Stand alone | Diversity analysis and visualization (needs similarity alignments as input). | http://ab.inf.uni-tuebingen.de/software/megan | [112] |
| 23. | QIIME | Stand alone | Data trimming and filtering, diversity analysis, and visualization. | http://qiime.org/ | [113] |
| 24. | Galaxy portal | Web based | Web repository of computational tools that can be run without informatic expertise. | https://usegalaxy.org/ | [1] |
| 25. | METAREP | Web server | Flexible comparative metagenomics framework. | http://www.jcvi.org/metarep/ | [114] |
| 26. | SmashCommunity | Stand alone | Performs assembly and gene prediction mainly for data from Sanger and 454 sequencing technologies. | http://www.bork.embl.de/software/smash/ | [115] |
| 27. | mothur | Stand alone | Fast processing of large sequence data. | http://www.mothur.org/ | [116] |
| 28. | RAMMCAP | Stand alone | Ultra fast sequence clustering and protein family annotation. | http://weizhonglab.ucsd.edu/rammcap/cgibin/rammcap.cgi | [117] |
| 29. | Phymm | Stand alone | Phylogenetic classification of metagenomic short reads usinginterpolated Markov models. | http://www.cbcb.umd.edu/software/phymm | [118] |
| 30. | MG-RAST | Web server | High-throughput pipeline for functional metagenomic analysis. | http://metagenomics.anl.gov/ | [119] |
| 31. | WebCARMA | Web server | Unassembled reads as short as 35 bp can be used for the taxonomic classification with less false positive prediction. | http://webcarma.cebitec.unibielefeld.de/ | [120] |
| 32. | CAMERA | Web server | Provides list of workflows for WGS data analysis. | https://portal.camera.calit2.net/gridsphere/gridsphere | [121] |
| 33. | CD-HIT | Web server | Identity-based clustering of sequences. | http://weizhonglab.ucsd.edu/cd-hit/ | [122] |
| 34. | TETRA | Web server | Correlation of tetra nucleotide usage patterns in DNA. | http://www.megx.net/tetra | [123] |