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NGSphy is a Python open-source tool for the genome-wide simulation of NGS data (read counts or Illumina reads) obtained from thousands of gene families evolving under a common species tree, with multiple haploid and/or diploid individuals per species, where sequencing coverage (depth) heterogeneity can vary among species, individuals and loci, including off-target and untargeted loci.

Related resources:

• Manual
  • PDF (Last version 20180214)
  • Older versions of the manual
• Getting started
• Validation and use case tests:
  • Validation test
  • Use case test
• Tutorials (Settings examples)
  • Read counts from a single gene tree
  • Illumina reads from a single gene tree, with ancestral sequence counts from a single gene tree
  • Read counts from a single gene tree, with anchored sequence counts from a single gene tree
  • Illumina reads from gene tree distribution counts from a single gene tree