Tag: Genetic Map

GMI 1.5 – Genetic Map Interpolator

GMI 1.5

:: DESCRIPTION

The GMI (Genetic Map Interpolator) package is designed to create interpolated genetic maps of single nucleotide polymorphism (SNP) markers. Starting from a list of single nucleotide polymorphism (SNP) rs numbers, GMI uses the R packages biomaRt and RMySQL to fetch the most up-to-date SNP and microsatellite physical positions from Ensembl, and then combines these with the Rutgers combined genetic and physical map to estimate the corresponding Kosambi genetic positions by linear interpolation for these SNPs.

::DEVELOPER

Division of Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  GMI

:: MORE INFORMATION

Chromonomer 1.13 – Genome Assembly with Genetic Map

Chromonomer 1.13

:: DESCRIPTION

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 identify scaffolds that have been incorrectly assembled according to the genetic map, and split those scaffolds.

DEVELOPER

Cresko labs

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Chromonomer

:: MORE INFORMATION

Citation:

Catchen J, Amores A, Bassham S.
Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny.
G3 (Bethesda). 2020 Nov 5;10(11):4115-4128. doi: 10.1534/g3.120.401485. PMID: 32912931; PMCID: PMC7642942.

ILPMap 20110128 – Construct Consensus Genetic Maps under Comparative Analysis

ILPMap 20110128

:: DESCRIPTION

ILPMap is a software of constructing consensus genetic maps in comparative analysis.

::DEVELOPER

Chen Xin , Yang Jian-Yi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • IBM ILOG CPLEX

:: DOWNLOAD

 ILPMap

:: MORE INFORMATION

Citation

X. Chen and J. Yang.
Constructing Consensus Genetic Maps in Comparative Analysis.
J Comput Biol. 2010 Nov;17(11):1561-73. Epub 2010 Oct 20.

CMap 1.01 – View Comparisons of Genetic & Physical Maps

CMap 1.01

:: DESCRIPTION

CMap (omparative Map Viewer) is a web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. A user can compare an unlimited number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession. CMap is freely available, can run on a variety of database engines and uses only free and open software components.

::DEVELOPER

the Generic Model Organism Database

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl 5.6.0 or higher
  • web server with CGI capabilites (e.g., Apache 1.x or 2.x)
  • A relational database, e.g. MySQL (4.0+), Sybase Adaptive Server Enterprise, PostgreSQL, SQLite or Oracle (9.x)
  • libgd 2.0.28 and GD.pm 2.15
  • Various Perl modules available on CPAN

:: DOWNLOAD

CMap ;  Documation

:: MORE INFORMATION

Citation

Ken Youens-Clark, Ben Faga, Immanuel V. Yap, Lincoln Stein and Doreen Ware
CMap 1.01: a comparative mapping application for the Internet.
, Bioinformatics 2009 25(22):3040-3042; doi:10.1093/bioinformatics/btp458.