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https://github.com/gokceneraslan/awesome-deepbio #DeepLearning #Bioinformatics #DeepBio

Chromosomer – a reference-based genome arrangement tool, which rapidly builds chromosomes from genome contigs or scaffolds using their alignments to a reference genome of a closely related species. Chromosomer does not require mate-pair...

Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of...

The accurate description and annotation of structural variants can be complex.  This is due to the different resolution that variants are reported from traditional cytogenetic coordinates down to the actual base pair positions....

A recombination map has been added for all multi-locus traits. The map positions (chromosomal) for neutral markers (e.g. SNPs) and loci under selection (QTLs, deleterious mutations, DMIs) can now be specified explicitly, or set at random....

Murasaki is an anchor alignment program that is exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 35 wall minutes), or 8 mammals in 21 CPU hours (42 wall minutes)) scalable (Arbitrarily parallelizable across multiple...

Strudel is our graphical tool for visualizing genetic and physical maps of genomes for comparative purposes. The application aims to let the user examine their data at a variety of different levels of resolution, from entire maps to individual...

DECIPHER is a software toolset that can be used to maintain, analyze, and decipher large amounts of DNA sequence data. To install DECIPHER, see the Downloads page. To begin using DECIPHER read the "Getting Started DECIPHERing" tutorial. Refer to the...

BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at:...