Recommended Microbiome Software
- QIIME2 – open source bioinformatics pipeline for microbiome analysis
- mothur – open source bioinformatics pipeline for microbiome analysis
- USEARCH – sequence analysis tool with search and clustering algorithms
- STAMP – statistical software for analyzing microbiome data
Recommended Genomics Software
- Galaxy – open source, web-based platform for a wide range of sequence and NGS data analyses
- CLC Genomics Workbench – integrated package with many basic alignment and analysis tools
- UGENE – open source integrated package for sequence analysis
- Chipster – integrated package for the analysis of NGS data, particularly RNAseq data
Recommended Alignment Software
- AliView – multiple sequence alignment viewer and editor
- MUSCLE – multiple sequence alignment program
- MAFFT – multiple sequence alignment program
Recommended Evolutionary Analysis Software
- MEGA – integrated package for evolutionary and phylogenetic analyses
- Phyloseq – an R package for analysis and graphic representation of OTU-clustered microbiome data
- BEAST – Bayesian evolutionary analyses using Markov chain Monte Carlo
- SplitsTree – program to compute unrooted phylogenetic trees or networks
- DnaSP – integrated package for population genetic analyses
- DAMBE – integrated package for evolutionary & phylogenetic analyses