www.molgen.mpg.de - Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous. Ranbow can also be applied to other polyploid genomes. After a first phasing,...
github.com - CSBFinder is a standalone Desktop java application with a graphical user interface, that can also be executed via command line.
CSBFinder implements a novel methodology for the discovery, ranking, and taxonomic distribution analysis of colinear...
github.com - MFannot is a program for the annotation of mitochondrial and plastid genomes
MFannot is a program for the annotation of mitochondrial and plastid genomes. It is a PERL wrapper around a set of diverse, external independent tools.
It makes intense...
catchenlab.life.illinois.edu - Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to...
github.com - PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes. Given an annotated genome it will use several approaches to identify the most likely prophage regions.
Initial versions of PhiSpy were written by
Sajia Akhter...
academic.oup.com - LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that...
synorth.genereg.net - Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic...
github.com - The k-mer Weighted Inner Product.
This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any...
ivory.idyll.org - DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lot of time thinking about how to store k-mer graphs efficiently, discard redundant data, and count them efficiently.
More recently, we've...
github.com - A simple, extensible, Perl script for producing figures of large phylogenetic trees.
While there are many other tree drawing programs, slacTree was originally written in 2009 to fill a need for producing publication quality figures of circular...