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Haplotype estimation tool for polyploids using NGS data of related individuals

Biosynthetic Genes Similarity Clustering and Prospecting Engine.

Defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index, a modified Domain Duplicate Score and the Adjacency Index)

R package for (e)QTL mapping

flow accumulation model made in R (and partly still in bash).

Arabidopsis eQTL analysis platform

Calculate the diversity of your gene clusters! Using hmmscan to find the pfam domains. Jaccard, DDS, GK as distance metrics including sequence similarity as a modifier. It outputs tab delimited network files that can be visualized in Cytoscape.

Simulation pipeline for generation of artificial polyploid genomes, estimation of their haplotypes from Next Generation Sequencing data using HapTree, HapCompass and SDhap, and finally evaluation of the estimation accuracy.

Scripts and resources used for my MSc Thesis at the Bioinformatics chair group.

The goal this project is to create a pipeline that automates the secondary metabolite phylogenetic analysis of fungi to a certain extent.

Several data files associated with the analysis of SMILES strings from the MIBiG database

Script for the published paper doi:10.1186/s12864-015-1733-8

ibrowser

Biosynthetic Genes Similarity Clustering and Prospecting Engine.

Defines a distance metric between Gene Clusters using a combination of three indices (Jaccard index, a modified Domain Duplicate Score and the Goodman-Kruskal gamma function)