:: DESCRIPTION
Hands On Genetics is a suite of interactive programs covering a wide range of topics in genetics.
Mendelian genetics:
SimpleGene, Mendelsim, SexLink, Punnett, GeneShare
Cytogenetics:
Meiosis
Molecular genetics:
Genetic molecules, PCR, Gelsim
Population genetics:
Popsim, Hardy-Weinberg, Fisher-Wright
::DEVELOPER
Hands On Genetics Editorial Board
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
LTR_STRUC is a new data-mining program that scans nucleotide sequence files for LTR retrotransposons and analyzes any resulting hits. Input files can be in fasta or NCBI flat file format.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
McCarthy, E.M., and J.F. McDonald. 2003.
LTR_STRUC: A novel search and identification program for LTR retrotransposons.
Bioinformatics 19: 362-367
:: DESCRIPTION
Molekel is an open-source multi-platform molecular visualization program.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
OSA (Ordered Subset Analysis Program ) allows the researcher to evaluate evidence for linkage even when heterogeneity is present in a data set. This is not an unusual occurrence when studying diseases of complex origin. Families are ranked by covariate values in order to test evidence for linkage among homogeneous subsets of families. Because families are ranked, a priori covariate cutpoints are not necessary. Covariates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, and so on.
::DEVELOPER
Duke Molecular Physiology Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hauser E.R., et al.
Ordered subset analysis in genetic linkage mapping of complex traits.
Genet. Epidemiol 2004;27:53-63
:: DESCRIPTION
CDPOP (Cost Distance POPulations) is a spatially-explicit simulator of gene-flow in complex landscapes to explain observed population responses and provide a foundation for landscape genetics.
::DEVELOPER
the Computational Ecology Lab, The University of Montana
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Landguth EL, Cushman, SA (2010)
CDPOP: A spatially-explicit cost distance population genetics program.
Molecular Ecology Resources 10, 156-161
:: DESCRIPTION
Endrov is a multi-purpose image analysis program. It is written indepedently and designed to address many of the shortcomings of ImageJ and many commercial packages. The sofware is a framework for image analysis and data analysis, aimed towards microscopy and the needs of current research.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nat Methods. 2013 Jun;10(6):454-6. doi: 10.1038/nmeth.2478.
Endrov: an integrated platform for image analysis.
Henriksson J, Hench J, Tong YG, Johansson A, Johansson D, Bürglin TR.
:: DESCRIPTION
LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.
::DEVELOPER
Miller Lab at Penn State University Center for Comparative Genomics and Bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Harris, R.S. (2007)
Improved pairwise alignment of genomic DNA.
Ph.D. Thesis, The Pennsylvania State University.
:: DESCRIPTION
RDP (Recombination detection program) is software that applies a number of recombination detection and analysis algorithms. Among other novelties, this version includes four new recombination analysis methods (3SEQ, VISRD, PHYLRO and LDHAT), new tests for recombination hot-spots, a range of matrix methods for visualizing over-all patterns of recombination within datasets and recombination-aware ancestral sequence reconstruction. Complementary to a high degree of analysis flow automation, RDP also has a highly interactive and detailed graphical user interface that enables more focused hands-on cross-checking of results with a wide variety of newly implemented phylogenetic tree construction and matrix-based recombination signal visualization methods. RDP can accommodate large datasets and is capable of analyzing alignments ranging in size from 1000×10 kilobase sequences to 20×2 megabase sequences within 48 h on a desktop PC.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P. (2010).
RDP3: a flexible and fast computer program for analyzing recombination.
Bioinformatics 26, 2462-2463
:: DESCRIPTION
BKChem is a free chemical drawing program.
::DEVELOPER
written by Beda Kosata , currently maintained by Reinis Danne.
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
BKChem is free software.
:: DESCRIPTION
BSMAP（Bisulfite Sequence Mapping Program）is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BSMAP: whole genome bisulfite sequence MAPping program.
Xi Y, Li W.
BMC Bioinformatics. 2009 Jul 27;10:232. doi: 10.1186/1471-2105-10-232.
Bioinformatics. 2012 Feb 1;28(3):430-2. doi: 10.1093/bioinformatics/btr668. Epub 2011 Dec 6.
RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing.
Xi Y, Bock C, Müller F, Sun D, Meissner A, Li W.
