Algorithms for Haplotype Assembly

  1. SDhaP, package for haplotype assembly based on semi-definite programming. Applicable to both diploids and polyploids (the latter may be bi-allelic or poly-allelic). The method is described in the following publication:

  2. AltHap, haplotype assembler based on matrix/tensor factorization. Significant speed improvement over competing methods. Details of the method can be found in the following publication:

  3. BFBP interprets haplotype assembly as the problem of decoding in communication systems and solves it via iterative belief propagation algorithm. Limited to bi-allelic variants. Details are in the following paper:

Software for Viral Quasispecies Reconstruction

  1. TenSQR is particularly suitable for reconstruction of viral quasispecies that consist of highly imbalanced populations (but applies more broadly). It relies on tensor factorization with successive read removal. Background is in the following article:

  2. QSdpR extends the ideas of SDhaP to the problem of reconstructing viral communities. For details about the method, please see the paper below:

  3. To reconstruct quasispecies characterized by very low diversity, aBayesQR combines ideas from unsupervised learning and Bayesian inference. Details are here: