| Molecular Genetics Related Sites |
|
| Site Name |
Description |
Clicks |
| QTL mapping software |
A QTL mapping software (in experimental crosses) in R environment. |
3731 |
| Haploview |
“Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses, like, haplotype population frequency estimation, single SNP and haplotype association tests, permutation testing for association significance, implementation of Paul de Bakker's Tagger tag SNP selection algorithm†etc. |
3432 |
| PyPop: Python for Population Genomics |
"PyPop (Python for Population Genomics) is an environment developed by the Thomson lab for doing large-scale population genetic analyses including: (1) conformity to Hardy-Weinberg expectations, (2) tests for balancing or directional selection; (3) estimates of haplotype frequencies (and their distributions) and measures and tests of significance for linkage disequilibrium (LD)". |
3031 |
| Haplotype analysis (HapStat) |
"HAPSTAT is a user-friendly software interface for the statistical analysis of haplotype-disease association. HAPSTAT allows the user to estimate or test haplotype effects and haplotype-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty and study design". |
2723 |
| Micro-Checker |
“Micro-Checker is a Windows application that checks for microsatellite null alleles and scoring errors. It also provides null allele estimates, and adjusts allele and genotypes frequenciesâ€. |
2611 |
| Microsatellite analyzer (MSA) 4.05 |
“MSA is a universal, platform independent, data analysis toolâ€. It has been “designed to handle large microsatellite data setsâ€. “Microsatellite analyzer calculates the standard suit of descriptive statistics and provides input files for other software packagesâ€. |
3335 |
| Microsatellite |
Micro-Checker is a Windows application that checks for microsatellite null alleles and scoring errors. It also provides null allele estimates, and adjusts allele and genotypes frequencies. |
2816 |
| Bayesian QTL mapping software for inbred lines |
Contains link to Bayesian QTL mapping software. |
2691 |
| Quantitative Trait Loci (QTL) Mapping Software |
Discussion and provision of links to some important QTL mapping software. |
2553 |
| Molecular Genetics Software Suites |
List of molecular genetic software (hyperlinked to the respective websites) pertaining to phylogenetics, primer deigning, population genetics, relatedness and parentage, restriction mapping etc., along with one line description. |
2932 |
| HelixTree |
Golden Helix is a commercial agency that provides several software for genetic-analysis and SNP analysis, DNAseq data analysis etc. |
2320 |
| NTSYSpc, Numerical Taxonomy System, Version 2.2 |
It is commercially available and is used to "discover pattern and structure in multivariate data". Thus it is helpful for clustering of data and dendogram construction (UPGMA based). |
3199 |
| GenAlEX 6.5 SOFTWARE |
"GenAlEx 6.5 (Peakall and Smouse 2006, 2012) offers a wide range of population genetic analysis options for the full spectrum of genetic markers within the Microsoft Excel environment on both PC and Macintosh computers". |
2839 |
| Real Time PCR Primer Sets |
This site contains the validated primer-sets for real time PCR in human, mouse and other species for various chemistries used in quantitative PCR. |
2836 |
| Human Mouse Homology Relationship |
Displays homology maps with reference to either human, or mouse or rat for "comparative mapping functions available in the Map Viewer". |
2483 |
| GeneCards |
"GeneCards is a searchable, integrated, database of human genes that provides concise genomic related information, on all known and predicted human genes". |
2255 |
| National Center for Genome Resources |
NCGR is US based non-profit organization that "offers Illumina® CSPro™ sequencing, analysis, assembly, annotation, genotyping and target enrichment services". |
3945 |
| PopGene |
Popgene is "a user-friendly computer freeware for the analysis of genetic variation among and within populations using co-dominant and dominant markers", developed by "Francis Yeh, Rongcai Yang and Timothy Boyle". |
2936 |
|
Top of Page
| Cytogenetics |
|
| Site Name |
Description |
Clicks |
| LUCIA Cytogenetics site. |
It is the website of the image analysis software (developed by Laboratory Imaging s.r.o.) for the cytogenetics laboratories. |
2402 |
| Cytogenetic Resources |
The site contains links to cytogenetic software, tutorials, FISH, educational resources Idiograms for several species. |
2523 |
|
Population vis-à-vis Statistical Genetics
Top of Page
| Population genetics |
|
| Site Name |
Description |
Clicks |
| Arlequin 3.11 |
Arlequin is "an Integrated Software for Population Genetics Data Analysis". |
4593 |
| Bottleneck version 1.2.02 |
"Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies". |
2376 |
| Genepop 4.0.10 |
"GENEPOP is a population genetics software package" originally developed by Michel Raymond and Francois Rousset. |
4705 |
| PLINK |
"PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses (with genotype/phenotype data) in a computationally efficient manner". |
2708 |
|
Top of Page
| Statistical Genetics |
|
| Site Name |
Description |
Clicks |
| Evo-Tutor |
It calculates and graphically displays various effects vis-Ã -vis amount of stochastic and deterministic factors as well as linkage equilibrium. |
2315 |
| Statistical genetics software guide |
It displays and introduces different online software on statistical genetics, viz. Genome Wide Association Programs, Haplotyping Programs, Linkage Analysis Programs, Pedigree Drawing Programs, Population Genetics Programs etc. |
10751 |
| Genetic Statistics Software |
The web page of Juan Pedro Steibel (Michigan State University) provides three useful software, namely, QpowR, %QPCR_MIXED and LD Estimate. |
2494 |
| Biostat software list |
A list of hyperlinked biostatistical software. |
2820 |
| Statistics Links |
Another link to statistical software, mixture modelling, data fitting software, time series analysis, probability etc. |
3266 |
| Genetic Analysis Software |
An exceptionally useful site enlisting the genetic software along with the relevant detail (full name, versions, description, authors, OS, website/ftp, source code etc). The software list has been arranged alphabatically. |
2427 |
| Animal Genomics Research |
It provides "links to Animal Genomics Research Web Sites and Database Resources". |
2250 |
|
Top of Page
| Breeding |
|
| Site Name |
Description |
Clicks |
| National Assoc.of Anim. Breeders E Guide |
It provides links to relevant sites that may be required by a breeder of domestic vis-Ã -vis pet animals. |
2280 |
| Pedigree Software |
A commercial agency (Tenset) that sells pedigree software like, Breeders Assistant, Pedserve, Pedigree Assistant. |
2572 |
| Zooeasy Software |
"ZooEasyâ„¢ Software (commercial) offers a unique all-in-one solution for the (semi-) professional breeder of specific animal species". |
2371 |
| ZooEasy Poultry Software |
A commercial agency that develops and sells poultry breeding software for selection of breeding pairs, pedigree management, medical results recording etc. |
2436 |
| Poultry Science Virtual Library |
It is virtual library that contains links to several resources of information on poultry management, breeding, genetics, several corporations and industries. |
2608 |
| Plant Breeding Software |
This site maintains plant breeding software, like, PLABSTAT, PLABQTL and PLABSTAT-PLABMQTL. |
2707 |
|
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