GEvolutionS – Genome Evolution Simulation

GEvolutionS

:: DESCRIPTION

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.

::DEVELOPER

N/A

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

GEvolutionS

:: MORE INFORMATION

N/A

 

UniMoG – Genome Rearrangement

UniMoG

:: DESCRIPTION

UniMoG (former DCJ) is a software tool unifying five genome rearrangement distance models: double cut and join (DCJ), restricted DCJ, Hannenhalli and Pevzner (HP), inversion only and translocation only. It allows computing all of these five distances between pairs of genomes represented as sequences of oriented common blocks.

DCJ (double-cut-and-join) computes the double-cut-and-join distance between two genomes and an optimal sorting scenario that transforms one genome into the other. It operates on the most general model of genomes with a mixed collection of linear and circular chromosomes. The sorting process includes all classical rearrangement operations such as inversions, translocations, transpositions, block interchanges, fusions and fissions.

::DEVELOPER

Rafael Friesen, Julia Mixtacki, Jens Stoye

:: SCREENSHOTS

UniMoG

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

DCJ

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Oct 1;28(19):2509-11. Epub 2012 Jul 18.
UniMoG–a unifying framework for genomic distance calculation and sorting based on DCJ.
Hilker R1, Sickinger C, Pedersen CN, Stoye J.

A. Bergeron, J. Mixtacki, J. Stoye.
A unifying view of genome rearrangements
Proceedings of WABI 2006, LNBI 4175, 163-173, 2006.

iDoComp 1.2 – Compression Scheme for Assembled Genomes

iDoComp 1.2

:: DESCRIPTION

iDoComp is an algorithm to compress re-sequenced assembled genomes, i.e., genomes for which an assembled genome of the same species already exists

::DEVELOPER

 Mikel Hernaez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • C Compiler

:: DOWNLOAD

 iDoComp

:: MORE INFORMATION

Citation

iDoComp: A Compression Scheme for Assembled Genomes.
Ochoa I, Hernaez M, Weissman T.
Bioinformatics. 2014 Oct 24. pii: btu698.

FastEP – Fast Computation of Entropic Profiles for the Detection of Conservation in Genomes

FastEP

:: DESCRIPTION

FastEP (Fast Entropic Profiler) is a linear time linear space algorithm suitable for large genomes and for the discovery of motifs with unbounded length.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 FastEP

:: MORE INFORMATION

Citation

M. Antonello, M. Comin,
Fast Computation of Entropic Profiles for the Detection of Conservation in Genomes“,
Proceedings of Pattern Recognition in Bioinformatics 2013,
Lecture Notes in BIoinformatics (LNBI) 2013, 7986, pp. 277–288.

Arachne 4.6233 – Whole-genome Shotgun Assembler

Arachne 4.6233

:: DESCRIPTION

ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments. It was designed for long reads from Sanger sequencing technology, and has been used extensively to assemble many genomes, including many that are large and highly repetitive.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Arachne

:: MORE INFORMATION

Citation

Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. 2002.
ARACHNE: a whole-genome shotgun assembler.
Genome Research12: 177–189.

Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. 2003.
Whole-genome sequence assembly for mammalian genomes: Arachne 2.
Genome Research 13: 91–96.

Gnerre S, Lander ES, Lindblad-Toh K, Jaffe DB. 2009.
Assisted assembly: how to improve a de novo genome assembly by using related species.
Genome Biology10: R88.

CNEFinder – Finding Conserved Non-Coding Elements in Genomes

CNEFinder

:: DESCRIPTION

CNEFinder is a tool for identifying conserved non-codings elements (CNEs) between two given DNA sequences with user-defined criteria.

:: DEVELOPER

Dr. Solon P. Pissis

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  •  Linux
  • C Compiler

:: DOWNLOAD

CNEFinder

:: MORE INFORMATION

Citation

Bioinformatics, 34 (17), i743-i747 (2018)
CNEFinder: Finding Conserved Non-Coding Elements in Genomes
Lorraine A K Ayad , Solon P Pissis , Dimitris Polychronopoulos

ASAP 1.4.1 – A Systematic Annotation Package for Community Analysis of Genomes

ASAP 1.4.1

:: DESCRIPTION

ASAP is designed to organize the data associated with a genome from the early stages of sequence annotation through genetic and biochemical characterization, providing a vehicle for ongoing updates of the annotation and a repository for genome-scale experimental data.

::DEVELOPER

Genome Evolution Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • PHP
  • MySQL

:: DOWNLOAD

 ASAP

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2003 Jan 1;31(1):147-51.
ASAP, a systematic annotation package for community analysis of genomes.
Glasner JD1, Liss P, Plunkett G 3rd, Darling A, Prasad T, Rusch M, Byrnes A, Gilson M, Biehl B, Blattner FR, Perna NT.

Badger 1.1 – An Accessible Genome Exploration Environment

Badger 1.1

:: DESCRIPTION

Badger provides an easy to use and intuitive way to explore and store genome data and gene predictions. It can be used as a central hub for genome projects allowing project members to search and access data as and when it is available. The database can hold multiple species, each with multiple genome versions and each genome with multiple gene prediction sets.

::DEVELOPER

The Blaxter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Badger

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 1;29(21):2788-9. doi: 10.1093/bioinformatics/btt466. Epub 2013 Aug 11.
Badger–an accessible genome exploration environment.
Elsworth B1, Jones M, Blaxter M.

 

Mauve 2.4.0 – Multiple Genome Alignments

Mauve 2.4.0

:: DESCRIPTION

Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics on a new scale. Aligning whole genomes is a fundamentally different problem than aligning short sequences.

Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours.

::DEVELOPER

The Darling Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 Mauve

:: MORE INFORMATION

Citation

Aaron C.E. Darling, Bob Mau, Frederick R. Blatter, and Nicole T. Perna. 2004.
Mauve: multiple alignment of conserved genomic sequence with rearrangements.
Genome Research. 14(7):1394-1403.

MetQy – Query Metabolic Functions of Genes and Genomes

MetQy

:: DESCRIPTION

MetQy (metabolic query) is a R package to ease interfacing with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to query metabolic functions of genes and genomes.

::DEVELOPER

OSS-Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOs
  • R

:: DOWNLOAD

MetQy

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Dec 1;34(23):4134-4137. doi: 10.1093/bioinformatics/bty447.
MetQy-an R package to query metabolic functions of genes and genomes.
Martinez-Vernon AS, Farrell F, Soyer OS