BOL

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...

genomicus.biologie.ens.fr - Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. Once a query gene has been entered, it...

github.com - evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation...

github.com - Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is...

github.com - AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are...

sourceforge.net - Metassembler combines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies. Genome assembly projects typically run multiple algorithms in an attempt to find the single best...

derisilab.ucsf.edu - We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively...

➜ bin git:(master) ✗ ls -l total 68 drwxrwxr-x 3 urbe urbe 4096 Jun 15 12:15 lib -rwxrwxrwx 1 urbe urbe 65141 Jun 15 17:13 LINKS ➜ bin git:(master) ✗ pwd /home/urbe/Tools/LINKS_1.8.6/bin ➜ bloomfilter git:(master) ✗ swig -Wall -c++...

FYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta...

chmille4.github.io - Scribl is a javascript, Canvas-based graphics library that easily generates biological visuals of genomic regions, alignments, and assembly data. Scribl can also be used in conventional offline pipelines, since everything needed to generate charts...