BOL

www.bx.psu.edu - We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map...

Interested in understanding the evolution of life. To obtain glimpses of such understanding, we employ existing and new methods of computational biology to perform research in several major...

scilifelab.github.io - SciLifeLab is a national center for molecular biosciences with focus on health and environmental research. Courses Old courses (2012-2014) Metagenomics Workshop 2015 November - Uppsala2016 November - Uppsala2017 November - Uppsala Introduction...

wishart.biology.ualberta.ca - CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature...

www.biostars.org - MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite...

github.com - Darwin-WGA, is the first hardware accelerator for whole genome alignment and accelerates the gapped filtering stage. Darwin-WGA also employs GACT-X, a novel algorithm used in the extension stage to align arbitrarily long genome sequences using a...

Our section develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. We aim to improve such foundational processes and translate emerging...

My main topics of interest are: The impact of non tree-like evolution such as horizontal gene transfers and hybridization on species biology Evolution and adaptation of animals in the absence of sexual reproduction and the underlying...

daehwankimlab.github.io - Resource for downloading all the HISAT2 related files  Please cite: Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915...

github.com - Generate unique k-mers for every contig in a FASTA file. Unique k-mer is consisted of k-mer keys (i.e. ATCGATCCTTAAGG) that are only presented in one contig, but not presented in any other contigs (for both forward and reverse strands). This tool...