Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolution
Broad area of research:
Genome Annotation and Functional Genomics
Bergman Lab is actively engaged in the development and application of computational methods to improve the annotation of functional biological features in genome sequences....
lce.biohpc.swmed.edu - GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various statistical methods to construct gene networks based on gene expression data and optional hub gene information.
It efficiently constructs gene...
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github.com - PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends...
In our research, we combine computational methods with an experimental component in a unified effort to develop comprehensive descriptions of genetic systems of cellular controls, including those whose malfunctioning becomes the basis of genetic...
github.com - This tutorial describes the usage of homologizer to phase gene copies into polyploid subgenomes. The tutorial is an abbreviated version of a soon-to-be published paper in Methods in Molecular Biology. Please see that paper for many more...
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http://mgra.cblab.org/ - MGRA (Multiple Genome Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and evolutionary history of extant genomes.
It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and...