Genome Comparison

• AGenDA Alignment-based Gene Detection Algorithm

  Gene prediction by cross-species sequence comparison.

• CEGeD Calculate Evolutionary Genome Distances

  The CEGeD program calculates the inversion- translocation- and double-cut-and-join-distance of two genomes and the corresponding optimal sorting scenarios that transforms one genome into the other. It is an extension of the DCJ-program.

• cg-cat Comparative Genomics - Contig Arrangement Toolsuite

  With current sequencing technologies, it is feasible to generate a lot of reads for a given genome. However, the assembly usually ends up in a set of contigs with gaps between them. If the sequences of one (or several) related genome(s) are already known, this information can be used to estimate the order and orientation of the contigs towards each other. This helps in the finishing phase of a sequencing project since it eases the design of specific primer sequences to fill the gaps.

• Gecko Gene cluster detection in prokaryotic genomes

  Gene cluster detection in prokaryotic genomes

• GEvolutionS Genome Evolution Simulation

  GEvolutionS simulates an evolutionary Genome rearrangement scenario with different genome rearrange operations. It operates on the most general model of genomes with a mixed collection on linear and circular genomes. The simulation process includes all classical rearrangement operations such as dcj, fissions, fusions, inversions, translocations, transpositions with choosable quantum.

• MGA Multiple Genome Aligner

  MGA efficiently computes multiple genome alignments of large, closely related DNA sequences.

• r2cat Related Reference based Contig Arrangement Tool

  With the help of next generation sequencing technologies it is feasible to generate a lot of reads for a given genome. However, the assembly usually ends up in a set of contigs with gaps between them. If a similar reference genome is known it the contigs can be mapped onto this and the size of the gaps can be estimated. This way, it is possible to design specific primer sequences to fill the gaps and finish the assembly. Description This is the tool r2cat, which maps contigs onto a reference genome using a q-gram filter. The contigs are ordered by a simple procedure and the result is visualized.

• REPuter Fast Computation of Maximal Repeats in Complete Genomes

  REPuter computes all maximal duplications and reverse, complemented and reverse complemented repeats in a DNA input sequence.

• SBBI Sorting by Block-Interchanges

  Say you are given a permutation of the numbers 1,?,n. The problem is to sort the permutation such that the numbers are in ascending order. The only operation you are allowed to perform is a block interchange, that is, you may take two blocks consisting of consecutive elements of the permutation and swap them.

• treecat phylogenetic TREE based Contig Arrangement Tool

  The phylogenetic tree based contig arrangement tool takes several genomes and their relationships in a phylogenetic tree into account to estimate a possible ordering of the contigs.

• UniMoG (former DCJ) Unified model of genomic distance computation via double cut and join (DCJ)

  UniMoG is a software tool unifying four genome rearrangement distance models: double cut and join (DCJ), Hannenhalli and Pevzner (HP), inversion only and translocation only. It allows computing all of these four distances between pairs of genomes. Furthermore, an optimal sorting scenario transforming the first genome of the pair into the second one is returned. All four models make use of the classical rearrangement operations and both linear and circular chromosomes can be handled dependent on the model. NOTE: The old DCJ tool is still available here, too.