GeneMiner2 is a comprehensive toolkit designed for phylogenomic genomics. Its main functionalities include:
- Mining single-copy nuclear genes, plastid genes/genomes, and other molecular markers from next-generation sequencing data.
- Aligning and trimming multiple molecular markers, constructing concatenated and coalescent-based phylogenetic trees, and calibrating tree time.

Reference for GeneMiner2:

Yu XY, Tang ZZ, Zhang Z, Song YX, He H, Shi Y, Hou JQ, Yu Y. 2026. GeneMiner2: Accurate and automated recovery of genes from genome-skimming data. Molecular Ecology Resources 26: e70111.https://doi.org/10.1111/1755-0998.70111

Features

  • target gene assembly
  • phylogenetic reconstruction
  • fine-grained read selection
  • adaptive k-mer selection

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2023-12-29
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