E-MEM 1.0.0 – Efficient computation of Maximal Exact Matches for very large Genomes

E-MEM 1.0.0

:: DESCRIPTION

E-MEM is a C++/OpenMP program designed to efficiently compute MEMs between large genomes.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 E-MEM

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 17. pii: btu687. [Epub ahead of print]
E-MEM: efficient computation of maximal exact matches for very large genomes.
Khiste N, Ilie L.

andi 0.10 – Estimating the Evolutionary Distance between closely related Genomes

andi 0.10

:: DESCRIPTION

andi is a  program for estimating the evolutionary distance between closely related genomes.

::DEVELOPER

Fabian Klötzl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 andi

:: MORE INFORMATION

Citation

andi: Fast and accurate estimation of evolutionary distances between closely related genomes.
Haubold B, Klötzl F, Pfaffelhuber P.
Bioinformatics. 2014 Dec 10. pii: btu815.

ANItools 2.0 – Calculating Average Nucleotide Identify (ANI) of pairs of Genomes

ANItools 2.0

:: DESCRIPTION

ANItools is a PERL scripts that can compare bacterial genomes and calculate their average nucleotide identity (ANI)

::DEVELOPER

National Institute for Communicable Disease Control and Prevention,china cdc

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ANItools

:: MORE INFORMATION

Citation:

J Gen Appl Microbiol. 2014;60(2):75-8.
Whole-genome sequence comparison as a method for improving bacterial species definition.
Zhang W1, Du P, Zheng H, Yu W, Wan L, Chen C.

CHROnicle 201503 – Reconstruction of the complete Evolutionary History of Genomes

CHROnicle 201503

:: DESCRIPTION

CHROnicle is a package dedicated to the reconstruction of the complete evolutionary history of genomes. It is based on the analysis of the marks accumulated over evolutionary time left in the genomes by chromosomal rearrangements. CHROnicle is composed of four different programs: SynChro, PhyChro, ReChro and AnChro.

::DEVELOPER

Laboratory of Computational and Quantitative Biology(LCQB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 CHROnicle

:: MORE INFORMATION

Citation

PLoS One. 2014 Mar 20;9(3):e92621. doi: 10.1371/journal.pone.0092621. eCollection 2014.
SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.
Drillon G1, Carbone A2, Fischer G

TSSV 0.2.5 – Characterization of Complex Allelic Variants in pure and mixed Genomes

TSSV 0.2.5

:: DESCRIPTION

TSSV (Targeted characterisation of Short Structural Variation) is a program that does targeted characterisation of short structural variation. It can be used for STR analysis, or any other type of targeted analysis. It characterises any variation between a set of user-defined markers.

::DEVELOPER

the ​Human Genetics department at ​Leiden University Medical Center.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

  TSSV

:: MORE INFORMATION

Citation

TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes.
Anvar SY, van der Gaag KJ, van der Heijden JW, Veltrop MH, Vossen RH, de Leeuw RH, Breukel C, Buermans HP, Verbeek JS, de Knijff P, den Dunnen JT, Laros JF.
Bioinformatics. 2014 Jun 15;30(12):1651-9. doi: 10.1093/bioinformatics/btu068

COSER – Compare Genomes with Segmental Duplications and Rearrangements

COSER

:: DESCRIPTION

COSER is a software to COmpare genomes with SEgmental duplications and Rearrangement

::DEVELOPER

Laboratory for Computational Biology and Bioinformatics (LCBB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 COSER

:: MORE INFORMATION

Citation

Comparing genomes with rearrangements and segmental duplications.
Shao M, Moret BM.
Bioinformatics. 2015 Jun 15;31(12):i329-i338. doi: 10.1093/bioinformatics/btv229.

MaxSSmap v1 – GPU program for Mapping Divergent Short Reads to Genomes with the Maximum Scoring Subsequence

MaxSSmap v1

:: DESCRIPTION

MaxSSmap is a GPU program with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. MaxSSmap identifies a local region of the genome followed by exact alignment.

::DEVELOPER

Usman Roshan

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MaxSSmap

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Nov 15;15:969. doi: 10.1186/1471-2164-15-969.
MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence.
Turki T1, Roshan U.

GENOMEPOP 2.7.4 – Evolve Populations of Genomes under complex Evolution Models and Demography

GENOMEPOP 2.7.4

:: DESCRIPTION

Genomepop is flexible software that allows the forward simulation of DNA sequences in a metapopulation context under a variety of conditions. Users can input their own sequences or tell the program to generate them. Retro and recurrent mutation can be allowed or neglected. A number of populations with any migration model can be defined. Each population consists of a number N of sequences or genomes.

::DEVELOPER

Antonio Carvajal-Rodriguez 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 GENOMEPOP

:: MORE INFORMATION

Citation

Antonio Carvajal-Rodriguez (2008)
GENOMEPOP: A program to simulate genomes in populations
BMC Bioinformatics 9: 223

PhyloSift 1.0.1 – Phylogenetic and Taxonomic Analysis for Genomes and Metagenomes

PhyloSift 1.0.1

:: DESCRIPTION

PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes.

::DEVELOPER

The Darling Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX

:: DOWNLOAD

 PhyloSift

:: MORE INFORMATION

Citation

PhyloSift: phylogenetic analysis of genomes and metagenomes.
Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA.
PeerJ. 2014 Jan 9;2:e243. doi: 10.7717/peerj.243.

SIGMA 1.0.2 – Strain-level Identification of Genomes from Metagenomic Analysis for Biosurveillance

SIGMA 1.0.2

:: DESCRIPTION

SIGMA is a novel sequence similarity-based approach for strain-level identification of genomes from metagenomic analysis for biosurveillance.

::DEVELOPER

Omics Bio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 SIGMA

:: MORE INFORMATION

Citation

Sigma: Strain-level Inference of Genomes from Metagenomic Analysis for Biosurveillance.
Ahn TH, Chai J, Pan C.
Bioinformatics. 2014 Sep 29. pii: btu641