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core-genome

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vinuesa / get_phylomarkers

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A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

bash r pipeline genomics perl phylogenetic-trees phylogenetics markers orthologues microbiology population-genetics codon-alignment maximum-likelihood phylogenomics species-trees recombination core-genome species-delimitation phylogenomics-pipeline clock-hypothesis
  • Updated Jan 7, 2025
  • Perl

JJChenCharly / OrthoSLC

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OrthoSLC: A pipeline to get Orthologous Genes using Reciprocal Best Blast Hit (RBBH) Single Linkage Clustering, indenpendent of relational database management system

lightweight bioinformatics genomics jupyter-notebook large-scale single-linkage-clustering large-dataset pan-genome core-genome dereplication pre-compiled reciprocal-blast-hits microbe-subspecies independent-of-mysql cpp-callable-binary convenient-installation
  • Updated Jan 6, 2025
  • Jupyter Notebook

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