Welcome to qdiv’s documentation!

qdiv is a python package for analyzing results from rRNA gene amplicon sequencing or similar data.

With qdiv you can subset and rarefy the data, generate a consensus table based on several count tables, calculate alpha- and beta diversity indices (focusing on Hill-based indices), plot a heatmap or PCoA, carry out null model analysis (Raup-Crick, NRI, NTI, beta NRI, and beta NTI, extended to all possible diversity orders), and run the Mantel- and Permanova tests.

Several scientific papers have been studied to program the algorithms used in qdiv. The key references can be found under Citations.

• Installation instructions
• Input files
• Load and print files
  • Loading files
  • Save files
  • Load new taxonomy
• Information and statistics
  • Get information
  • Mantel test
  • Permanova
  • Distance between sequences
• Subset and manipulate data
  • Subset to specific samples
  • Subset to specific OTUs/ASVs
  • Subset to the most abundant OTUs/ASVs
  • Subset based on taxonomic classification
  • Merge samples
  • Rarefy
  • Consensus table
  • Merge objects
• Diversity calculations
  • Alpha diversity
  • Beta diversity (dissimilarity)
  • Evenness
• Null models
  • Raup-Crick
  • Phylogenetic null models
• Plotting
  • Heatmap
  • Alpha diversity
  • PCoA
  • Pairwise dissimilarity
  • Rarefaction curve
  • Octave (frequency histogram)
  • Dissimilarity contributions of taxa
• Citations
• Tutorial 1
  • TABLE OF CONTENTS
  • PREPARE THE DATA FILES
  • A FIRST LOOK AT THE DATA
  • RAREFYING
  • ALPHA DIVERSITY
  • BETA DIVERSITY

• Search Page