Cri-Map 2.4 – Construct Multilocus Linkage Map

Cri-Map 2.4

:: DESCRIPTION

CRI-MAP‘s purpose is to allow rapid, largely automated construction of multilocus linkage maps (and facilitate the attendant tasks of assessing support relative to alternative locus orders, generating LOD tables, and detecting data errors). Although originally designed to handle codominant loci (e.g. RFLPs) scored on pedigrees “without missing individuals”, such as CEPH or nuclear families, it can now (with some caveats described below) be used on general pedigrees, and some disease loci.

::DEVELOPER

Matise Laboratory of Computational Genetics.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows wity Cygwin /MacOsX
GCC

:: DOWNLOAD

CRI-MAP

:: MORE INFORMATION

Citation

Hum Hered. 1995 Mar-Apr;45(2):103-16.
Parallel computation of genetic likelihoods using CRI-MAP, PVM, and a network of distributed workstations.
Matise TC, Schroeder MD, Chiarulli DM, Weeks DE.

LPmerge 1.7 – Merging Linkage Maps by Linear programming

LPmerge 1.7

:: DESCRIPTION

LPmerge is an R package for building consensus maps across multiple populations through linear programming (LP).

::DEVELOPER

Endelman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R

:: DOWNLOAD

LPmerge

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 1;30(11):1623-4. doi: 10.1093/bioinformatics/btu091. Epub 2014 Feb 14.
LPmerge: an R package for merging genetic maps by linear programming.
Endelman JB1, Plomion C2.

HighMap – Construction and Analysis of High-density Linkage Map

HighMap

:: DESCRIPTION

HighMap software is suitable for genetic map. This software utilized maximum likelihood and smooth algorithm, and could deal with ten thousand markers that make map distance more stably.

::DEVELOPER

Biomarker Technologies Corporation

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Construction and analysis of high-density linkage map using high-throughput sequencing data.
Liu D, Ma C, Hong W, Huang L, Liu M, Liu H, Zeng H, Deng D, Xin H, Song J, Xu C, Sun X, Hou X, Wang X, Zheng H.
PLoS One. 2014 Jun 6;9(6):e98855. doi: 10.1371/journal.pone.0098855.

IRILmap 1.1 – Linkage Map Distance Sonversion software

IRILmap 1.1

:: DESCRIPTION

IRILmap (Intermated recombinant inbred lines Map) was developed to compute “actual” centiMorgan distances from MapMaker output files (result of “Map” command obtained with the “photo” command) obtained from IRIL data with “RI self” or “RI sib” options (see “Distance calculation” section for details). It is also possible to use IRILmap to convert Haldane distances into Kosambi’s, or reciprocally. Mapping data produced with other software than MapMaker can be used, provided that file formats are respected (see “Format specifications” section for details) and that distances were computed as for RILs by using Haldane & Waddington’s formula. For this purpose, tabulated files are also accepted in addition to MapMaker output files.

:: DEVELOPER

UMR Plant Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

IRILmap

:: MORE INFORMATION

Citation:

Falque M.
IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains.
Bioinformatics. (2005) Aug 15;21(16):3441-2

MapInspect – Compare & Display Linkage Maps

MapInspect

:: DESCRIPTION

Mapinspect features Map Comparison, marker highlighting and graphical display of Pair-wise recombination estimates on the final map.

MapInspect can display, print and save these images, and has no limit to the number of maps it can compare (but only neighbouring maps are compared). Maps can be flipped within MapINspect, an the on-screen order of the maps can be changed.

::DEVELOPER

Wageningen UR Plant Breeding

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

MapInspect

:: MORE INFORMATION

Record 2.0 – Arranging Markers into Linear Order

Record 2.0

:: DESCRIPTION

RECORD (REcombination Counting and ORDering) can be used for the ordering of loci on genetic linkage maps. The method minimises the total number of recombination events. The search algorithm is a heuristic procedure, combining elements of branch-and-bound with local reshuffling.

Since the criterion does not require intensive calculations, the algorithm rapidly produces an optimal ordering as well as a series of near-optimal ones. The latter provides insight into the local certainty of ordering along the map.

RECORD can deal with the following types of mapping populations: BC1, F2, F3, RILs (in fact any generation obtained by repeated selfing of a hybrid between homozygous parents). Mapping populations from non-inbreds should be split into BC1 or HAP data that represent the maternal and paternal gametes, according to the two-way pseudo-testcross method. Please provide the data in a .LOC file in JoinMap format.

::DEVELOPER

Wageningen UR Plant Breeding

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

RECORD

:: MORE INFORMATION

Citation

RECORD: a novel method for ordering loci on a genetic linkage map.
Van Os H, Stam P, Visser RG, Van Eck HJ.
Theor Appl Genet. 2005 Dec;112(1):30-40. Epub 2005 Oct 14. Erratum in: Theor Appl Genet. 2006 Jan;112(2):389.

MapChart 2.2 – Graphical Presentation of Linkage Maps and QTLs

MapChart 2.2

:: DESCRIPTION

MapChart is a Windows software for the graphical presentation of linkage maps and QTLs. These charts are composed of a sequence of vertical bars representing the linkage groups or chromosomes. On these bars the positions of loci are indicated, and next to the bars QTL intervals and QTL graphs can be shown. MapChart reads the linkage information (i.e. the locus and QTL names and their positions) from text files.

::DEVELOPER

dr. RE (Roeland) Voorrips

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

MapChart

:: MORE INFORMATION

Citation:

Voorrips, R.E., 2002.
MapChart: Software for the graphical presentation of linkage maps and QTLs.
The Journal of Heredity 93 (1): 77-78.

TetraploidMap 1.0.6 – Calculate Linkage Maps for Autotetraploid Populations

TetraploidMap 1.0.6

:: DESCRIPTION

TetraploidMap is a graphical user interface for calculating linkage maps for autotetraploid populations. It is suitable for handling markers scored on two parents and the full-sib offspring of a cross between them. TetraploidMap handles both codominant and dominant molecular markers, in all possible configurations, and takes into account the presence of null alleles in the analysis. It now includes a routine for QTL mapping.

::DEVELOPER

Christine Hackett at Biomathematics and Statistics Scotland (BioSS)

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

TetraploidMap

:: MORE INFORMATION

Citation

Hackett, C.A.Milne, I., Bradshaw, J.E. & Luo, Z.W. 2007.
TetraploidMap for Windows: linkage map construction and QTL mapping in autotetraploid species.
Journal of Heredity 98, 727-729.