DeGiorgio Group GitHub Page
ANDES (ANomaly DEtection using Summary statistics)
A program that implements the anomaly detection model ANDES of Kanjilal et al. for uncovering aberrant genomic regions by modeling genomic autocovariation with functional data analysis.
α-DAWG (α-molecules for Detecting Adaptive Windows in Genomes)
A Python program that implements the classifier α-DAWG of Amin et al. (2024) for identifying adaptive windows through α-molecule basis expansion of haplotype alignment images.
CLOUDe (CLassification using Ornstein-Uhlenbeck of Deletions)
An R program that implements the suite of machine learning methods CLOUDe of Campelos dos Santos et al. (2024) for predicting evolutionary targets of gene deletion events from expression data in two species.
ROBRT (ROBustRegression on Trees)
An R program that estimates trait association on phylogenetic trees using the robust L1, M, S, and MM phylogenetic independent contrast regression estimators of Adams et al. (2023).
T-REx (Tensor decomposition-based Robust feature Extraction and classification)
A Python program that implements the classifier T-REx of Amin et al. (2023) for identifying adaptive regions through tensor decomposition of images of haplotype alignments.
SpeciesTopoTestR
An R program that computes the KH*, SH*, and SOWH* likelihood tests of species topology hypotheses of Adams and DeGiorgio (2023).
SISSSCO (Spectral Inference of Summary Statistic Signals using COnvolutional neural networks)
A Python program that implements the classifier SISSSCO of Arnab et al. (2023) for identifying adaptive regions through spectral analysis of summary statistic signals.
LASSI-Plus
A program written in C++ that implements the likelihood ratio Λ statistic of DeGiorgio and Szpiech (2021) for detecting selective sweeps and inferring their softness using the spatial distribution of distortions in the haplotype frequency spectrum. Software hosted by collaborator Zachary Szpiech.
BalLeRMix+
A Python program that can simultaneously perform genomic scans of positive selection and long-term balancing selection using the composite likelihood ratio B statistics of Cheng and DeGiorgio (2022).
funbiased
A Python script that computes the unbiased estimators of F2, F3, normalized F3, and normalzied F4 statistics of Mughal and DeGiorgio (2021).
PRDATR (PRobabilistic Distances under models of Adaptive Trait evolution in R)
An R program that computes the probabilistic distances between phylogenetic models of continuous trait evolution of Adams et al (2021).
PhyloWGA
An R program for performing chromosome-aware phylogenetic interrogation of whole genome alignments of Adams et al (2021).
CLOUD (CLassification using Ornstein-Uhlenbeck of Duplicates)
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.
SURFDAWave (Sweep inference Using Regularized FDA with Wavelets)
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.
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).
BalLeRMix (BALancing selection LikElihood Ratio MIXture models)
A Python script that can perform genomic scans for balancing selection using the composite likelihood ratio B statistics of Cheng and DeGiorgio (2020).
LASSI (Likelhood-based Approach for Selective Sweep Inference)
A Python script that implements the likelihood ratio T statistic of Harris and DeGiorgio (2020) for detecting selective sweeps and inferring their softness.
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.
TASTI (Taxa with Ancestral structure Species Tree Inference)
An R program that implements the maximum likelihood estimator of species trees in the presence of ancestral population structure of Koch and DeGiorgio (2020).
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.
MULLET (MULti-species LikElihood Tests)
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).
MuteBaSS (MUlTi-spEcies BAlancing Selection Summaries)
A Python script that computes multi-species variants of HKA and NCD for detecting long-term balancing selection from Cheng and DeGiorgio (2019).
CalcABS
A Python script that can perform genomic scans for ancestral selective sweeps using the ancestral branch statistic (ABS) of Cheng et al. (2017).
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.
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).
BALLET (BALancing selection LikElihood Test)
A program written in C that can perform genomic scans for balancing selection using the composite likelihood ratio tests of DeGiorgio et al. (2014).