mdegiorgio
DeGiorgio Group software packages that implement statistical, machine learning, and signal processing methods for studying evolution from genomes.
Florida Atlantic UniversityBoca Raton, FL
Pinned Repositories
AlphaDAWG
Implementation of the sweep classifier of Hasan et al., where images of haplotype alignments are decomposed using alpha-molecule basis expansions
ANDES
A program that implements the anomaly detection model ANDES of Kanjilal et al. (submitted) for uncovering aberrant genomic regions by modeling genomic autocovariation with functional data analysis.
BalLeRMix
Software package for BalLeRMix and scripts used in the study "Flexible mixture model approaches that accommodate footprint size variability for robust detection of balancing selection" (Cheng & DeGiorgio 2020)
BallerMixPlus
This repository hosts the software package for BalLeRMix+, an extension of BalLeRMix that can jointly detect recent positive selection and long-term balancing selection.
BALLET
A program written in C that can perform genomic scans for balancing selection using the composite likelihood ratio tests of DeGiorgio et al. (2014). For simulated frequency spectra and results of empirical scans, visit http://degiorgiogroup.fau.edu/ballet.html
BestHet
An R script that computes the unbiased estimator of expected heterozygosity of Harris and DeGiorgio (2017) at a locus, as well as Fst and the locus-specific branch length, which are functions of expected heterozygosity.
CalcABS
A Python script that can perform genomic scans for ancestral selective sweeps using the ancestral branch statistic (ABS) of Cheng et al. (2017).
CLOUD
An R program that implements the multi-layer neural network method CLOUD of DeGiorgio and Assis (2021) for classifying duplicate gene retention mechanisms and predicting their evolutionary parameters from gene expression data in two species.
SweepFinder2
A program written in C that can perform genomic scans for recent selective sweeps selection while controlling for background selection and mutation rate variation (DeGiorgio et al. 2016).
VolcanoFinder
A program written in C that can perform genomic scans for adaptive introgression using the composite likelihood ratio test of Setter et al. (2020).
mdegiorgio's Repositories
mdegiorgio/SweepFinder2
A program written in C that can perform genomic scans for recent selective sweeps selection while controlling for background selection and mutation rate variation (DeGiorgio et al. 2016).
mdegiorgio/VolcanoFinder
A program written in C that can perform genomic scans for adaptive introgression using the composite likelihood ratio test of Setter et al. (2020).
mdegiorgio/AlphaDAWG
Implementation of the sweep classifier of Hasan et al., where images of haplotype alignments are decomposed using alpha-molecule basis expansions
mdegiorgio/ANDES
A program that implements the anomaly detection model ANDES of Kanjilal et al. (submitted) for uncovering aberrant genomic regions by modeling genomic autocovariation with functional data analysis.
mdegiorgio/BalLeRMix
Software package for BalLeRMix and scripts used in the study "Flexible mixture model approaches that accommodate footprint size variability for robust detection of balancing selection" (Cheng & DeGiorgio 2020)
mdegiorgio/BallerMixPlus
This repository hosts the software package for BalLeRMix+, an extension of BalLeRMix that can jointly detect recent positive selection and long-term balancing selection.
mdegiorgio/BALLET
A program written in C that can perform genomic scans for balancing selection using the composite likelihood ratio tests of DeGiorgio et al. (2014). For simulated frequency spectra and results of empirical scans, visit http://degiorgiogroup.fau.edu/ballet.html
mdegiorgio/BestHet
An R script that computes the unbiased estimator of expected heterozygosity of Harris and DeGiorgio (2017) at a locus, as well as Fst and the locus-specific branch length, which are functions of expected heterozygosity.
mdegiorgio/CalcABS
A Python script that can perform genomic scans for ancestral selective sweeps using the ancestral branch statistic (ABS) of Cheng et al. (2017).
mdegiorgio/CLOUD
An R program that implements the multi-layer neural network method CLOUD of DeGiorgio and Assis (2021) for classifying duplicate gene retention mechanisms and predicting their evolutionary parameters from gene expression data in two species.
mdegiorgio/CLOUDe
CLOUDe is an R implementation of Campelo dos Santos et al suite of machine learning methods for predicting evolutionary targets of gene deletion events from expression data in two species.
mdegiorgio/funbiased
A Python script that computes the unbiased estimators of F2, F3, normalized F3, and normalzied F4 statistics of Mughal and DeGiorgio (2021).
mdegiorgio/LASSI
A Python script that implements the likelihood ratio T statistic of Harris and DeGiorgio (2020) for detecting selective sweeps and inferring their softness.
mdegiorgio/lassip
LASSI-Plus: A program to calculate haplotype frequency spectrum statistics
mdegiorgio/MULLET
A program written in C that can perform scans for ancient multi-species balancing selection in the absence of trans-species polymorphism using the composite likelihood ratio tests of Cheng and DeGiorgio (2019). For simulated frequency spectra and results of empirical scans, visit http://degiorgiogroup.fau.edu/mullet.html
mdegiorgio/MuteBaSS
Software package for computing summary statistics designed for trans-species balancing selection (Cheng and DeGiorgio, 2019).
mdegiorgio/PhyloWGA
PhyloWGA: user-friendly R package for improving chromosome-scale phylogenetic analyses
mdegiorgio/PRDATR
PRDATR: Probabilistic distances between phylogeny-aware models of continuous trait evolution
mdegiorgio/ROBRT
ROBRT: ROBust Regression on Trees
mdegiorgio/SISSSCO
A Python program that implements the classifier SISSSCO of Arnab et al. (2022) for identifying adaptive regions through a time-frequency analysis of summary statistic signals.
mdegiorgio/SpeciesTopoTestR
SpeciesTopoTestR: Likelihood-based hypothesis tests of species topologies in R
mdegiorgio/SS-X12
A Python script that implements the classifier SS-H12 of Harris and DeGiorgio (2020) for detecting shared selective sweeps, and classifying them as ancestral or covergenent, as well as hard or soft.
mdegiorgio/SURFDAWave
An R program that implements the classifier and predictor SURFDAWave of Mughal et al. (2020) for identifying adaptive targets and learning their evolutionary parameters using the spatial distribution of summary statistics around a test site. For results of empirical scans, visit http://degiorgiogroup.fau.edu/surfdawave.html
mdegiorgio/T-REx
Tensor decomposition based feature extraction and classification to detect natural selection from genomic data
mdegiorgio/TASTI
Taxa with Ancestral structure Species Tree Inference
mdegiorgio/Trendsetter
A Python script that implements the classifier Trendsetter of Mughal and DeGiorgio (2019) for classifying genomic regions as neutral, hard sweep, or soft sweep using the spatial distribution of summary statistics around a test site. For results of empirical scans, visit http://degiorgiogroup.fau.edu/trendsetter.html