Recommended Software

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
  • BEASTBayesian 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