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    34 repositories

    • beast-phylonco

      Public
      A BEAST2 package for single-cell cancer evolution
      Java
      •
      GNU Lesser General Public License v2.1
      •5•8•26•1•Updated Apr 14, 2026Apr 14, 2026

    • tetres

      Public
      Package for discrete time trees
      Python
      •
      MIT License
      •0•3•1•0•Updated Mar 16, 2026Mar 16, 2026

    • lab

      Public
      Biological Data Science Lab website
      data-sciencegenomicsalgorithms
      data-sciencegenomicsalgorithmsbiologymathematics
      HTML
      •0•0•1•0•Updated Mar 15, 2026Mar 15, 2026

    • skyline-stratigraphic-ranges

      Public
      Java
      •0•2•0•0•Updated Feb 3, 2026Feb 3, 2026

    • snvformer_v2

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

    • snvformer

      Public
      Python
      •
      MIT License
      •1•3•1•0•Updated Aug 19, 2025Aug 19, 2025

    • vcf2fasta

      Public
      Python
      •1•3•4•1•Updated Jun 12, 2025Jun 12, 2025

    • KAN_for_GP

      Public
      Python
      •0•0•0•0•Updated May 28, 2025May 28, 2025

    • linguaPhyloSR

      Public
      LinguaPhylo: A language for describing, visualising and simulating probabilistic phylogenetic models
      Java
      •
      GNU Lesser General Public License v3.0
      •7•0•0•0•Updated May 12, 2025May 12, 2025

    • skyline-SRFBD-validation

      Public
      R
      •0•0•0•0•Updated Apr 29, 2025Apr 29, 2025

    • fossilsim

      Public
      R package for simulating fossil data on phylogenetic trees under mechanistic models of preservation and sampling
      HTML
      •4•1•0•0•Updated Apr 2, 2025Apr 2, 2025

    • TreeSim

      Public
      TreeSim — Simulating Phylogenetic Trees
      R
      •1•1•0•0•Updated Apr 2, 2025Apr 2, 2025

    • Centroid-Code

      Public
      This repository contains a Python implementation of the Centroid algorithm and a script to generate simulated datasets.
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 24, 2025Feb 24, 2025

    • KAN-for-Binary-Phenotype-Classification

      Public
      TeX
      •0•0•0•0•Updated Nov 23, 2024Nov 23, 2024

    • FBD-dLTTs

      Public
      Simulations for identifiability paper
      R
      •0•0•0•0•Updated Aug 28, 2024Aug 28, 2024

    • VSTExprPhylo

      Public
      Scripts and analyses in Visium Spatial Transcriptomics phylogenetic analyses paper
      R
      •0•0•0•0•Updated Jun 12, 2024Jun 12, 2024

    • Pint

      Public
      Fast interactions lasso for sparse data
      C
      •
      MIT License
      •0•6•0•0•Updated Mar 26, 2024Mar 26, 2024

    • castor

      Public
      Castor fork for sampled ancestor trees
      C++
      •1•0•0•0•Updated Jan 21, 2024Jan 21, 2024

    • mixed_speciation_stratigraphic-ranges

      Public
      Java
      •6•0•0•0•Updated Dec 19, 2023Dec 19, 2023

    • rrnni

      Public
      R package for RNNI distance
      cranrphylogenetics
      cranrphylogeneticsr-packager-stats
      C
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Aug 25, 2023Aug 25, 2023

    • rankedSPR

      Public
      Code for the ranked SPR paper, mostly experiments on diameters and shortest paths
      Python
      •
      MIT License
      •1•1•1•0•Updated May 16, 2023May 16, 2023

    • treeOclock

      Public
      Implementation of algorithms in the RNNI space, e.g. FINDPATH
      C
      •
      MIT License
      •1•4•0•0•Updated Apr 3, 2023Apr 3, 2023

    • seidel_compressed

      Public
      Seidel's Algorithm using Compressed Matrices (TurboPFor)
      C
      •0•0•0•0•Updated Jan 30, 2023Jan 30, 2023

    • RNNI_code

      Public
      Python
      •0•1•1•0•Updated Jan 30, 2023Jan 30, 2023

    • lasso_data_processing

      Public
      R
      •0•0•0•0•Updated Oct 23, 2022Oct 23, 2022

    • dct_parser

      Public
      Python
      •0•0•0•0•Updated Sep 8, 2022Sep 8, 2022

    • beast-phylonco-paper

      Public
      Data and analysis scripts to accompany BEAST phylonco
      Python
      •0•1•0•0•Updated Aug 21, 2022Aug 21, 2022

    • phyloRNA

      Public
      A package to facilitate a phylogenetic analysis of scRNAseq data
      R
      •
      Other
      •1•7•0•0•Updated Jul 28, 2022Jul 28, 2022

    • phyloRNAanalysis

      Public
      A phylogenetic analysis from scRNA-seq data using both expression levels and identified SNVs
      R
      •1•8•1•0•Updated Jun 8, 2022Jun 8, 2022

    • beter

      Public
      R package to programatically create BEAST2 XMLs
      R
      •
      Other
      •0•2•1•0•Updated Jun 2, 2022Jun 2, 2022
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