Yongtao Guan

Software

ReKo: Reflection Knockoffs via Householder Reflection (2025)

ReKo constructs knockoffs of an n by p feature matrix using Householder Reflection. By introducing ghost observation corresponding to priors for Householder reflection, ReKo works for both n > p and n < p.
Source code and Mannual on github

IDUL: Iterative dispersion udpate to fit linear mixed model (2024)

IDUL is designed for multi-omics analysis where each SNPs are tested for association with many phenotypes. IDUL has both theoretical and practical advantages over the Newton-Raphson method. Manuscript will be available shortly.
IDUL Linux Excutable (Version 0.83)
Source code and Mannual on github

Kindred: Infer kinship and inbreeding coefficients (2023)

Kindred is designed to infer kinship phi between a pair of samples accounting for inbreeding of the samples. This is done through modelling nine latent Jacquard IBD states. If the pair is one and itself, the kinship is phi = (1+F)/2 where F denotes inbreeding coefficient. Manuscript will be available shortly.
Kindred Linux Excutable (tarred)
Kindred Mac Executable (tarred)
Source code and Mannual on github

Nubeam-dedup de-duplicate sequencing reads without mapping (2020)

Nubeam-dedup represents nucleotides by matrices, transforms reads into products of matrices, and based on which assigns a unique number to a read. Thus, duplicate reads can be efficiently removed by using a collisionless hash function. This is the companion software for the paper Nubeam-dedup Bioinforamtics.
Download and Documentation on github

Bach: Bausch's algorithm for chi-squared weighted sum (2018)

This software computes tail probability of a mixture of chi-squared random variables. We (I mean former graduate stuent Quan Zhou) implmented Bausch's algorithm using GNU GMP library so that a tail probability (or p-value) can be evaluated to an arbitrary precision. It is the companion software for a manuscript written by Zhou and Guan Null distribution of Bayes factors.
Download and Documentation

ELAI: Efficient Local Ancestry Inference (2014)

The software performs local ancestry inference for admixed individuals. It is the companion software for the paper Local ancestry inference.
Download and Documentation on github
New multi-threading ELAI

hapQTL: haplotype Quantitative Loci (2014)

This software performs association testing between local haplotypes and phenotypes at each core marker. It is the companion software for the paper Haplotype QTL.
Download and Documentation

piMASS: posterior inference via Model Averaging and Subset Selection (2010)

The software performs genome-wide joint analysis of all SNPs in association with a phenotype. We use Markov chain Monte Carlo to perform subset selection and model averaging. This is the companion software for the paper Bayesian variable selection regression.
Download and Documentation

BIMBAM: Baysian Imputation Based Association Mapping (2008)

The software performs genotype imputation and statistical tests for disease association, including single SNP tests and regional multi-SNP tests. This is the companion software for the paper Practical issues in imputation.
Download and Documentation

WinSSS: Windows-based Stochastic Spatial Simulator (2004)

This is a Windows-based software. It implements many classical models in interacting particle systems, for example, the multiple contact process, the Greenberg Hastings process, and the generalized Rock-Scissor-Paper dynamic. The real time animations are rendered by openGL.
Download and Documentation
Source code for WinSSS