| description | ALOHOMORA is a software tool designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels |
| version | 0.33 |
| homepage | http://gmc.mdc-berlin.de/alohomora/ |
| commands | alohomora allegro_errors.pl gh_snp_info.pl merlin_lod.pl allegro_lod.pl gh_snp_lod.pl merlin_npl.pl allegro_npl.pl gh_snp_npl.pl merlin_qtl_plot.pl allegro_scan_start.pl gh_snp_qtl_plot.pl merlin_qtl_start.pl allegro_start.pl gh_snp_qtl_start.pl merlin_scan_start.pl fbat_plot.pl gtype2alohomora.pl merlin_start.pl fbat_start.pl mega2sw_haplo_start.pl plink_start.pl gh_errors.pl mega2sw_lod_start.pl sib_tdt_plot.pl gh_snp_fam_lod.pl mergeGDASfiles.pl sib_tdt_scan_start.pl gh_snp_fam_npl.pl merlin_errors.pl sw_snp_lod.pl gh_snp_hlod.pl merlin_lod2map.pl wiped_npl.pl |
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| description | Genetic Analysis Software |
| version | 4.1P |
| homepage | http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/fastlink.html |
| commands | ckpt ilink linkmap lodscore mlink unknown |
| manpages | ckpt ilink linkmap lodscore mlink unknown |
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| description | kisSnp compares two sets of NGS raw reads, detecting Single Nucleotide Polymorphism occurring between the two sets |
| version | 1.05 |
| homepage | http://alcovna.genouest.org/kissnp-page/ |
| commands | kissnpcheckreads kisSnp_two_sets compare_two_sets.sh |
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| description | software for finkage and Association Modeling in Pedigrees. LAMP uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees |
| version | 0.0.9 |
| homepage | http://www.sph.umich.edu/csg/abecasis/LAMP/ |
| commands | lamp |
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| description | MACH 1.0 is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. |
| version | 1.0.16 |
| homepage | http://www.sph.umich.edu/csg/yli/match/index.html |
| commands | mach1 thunder |
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| description | Programs for genetic linkage analysis and mapping genes underlying complex traits. |
| version | 3 |
| homepage | http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/ |
| commands | mapmaker qtl |
| manpages | mapmaker qtl |
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| description | MERLIN uses sparse trees to represent gene flow in pedigrees. |
| version | 1.1.2 |
| homepage | http://www.sph.umich.edu/csg/abecasis/Merlin/ |
| commands | merlin merlin-offline merlin-regress minx minx-offline pedwipe pedmerge hapmapConverter |
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| description | Detecting marker typing incompatibilities in pedigree data |
| version | 1.1 |
| homepage | http://watson.hgen.pitt.edu/register/ |
| commands | pedcheck_platform |
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| documentation |
http://watson.hgen.pitt.edu/register/docs/pedcheck.html |
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| description | PEDSTATS is a tool for quick validation and summary of any pair of pedigree and data files. |
| version | 0.6.12 |
| homepage | http://www.sph.umich.edu/csg/abecasis/PedStats/ |
| commands | pedstats |
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| description | Joint Linkage and/or Linkage Disequilibrium Analysis |
| version | 1.0.6b |
| homepage | http://www.helsinki.fi/~tsjuntun/pseudomarker/ |
| commands | pseudomarker twostage.py |
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| description | SimWalk2 is a statistical genetics computer application for haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD) and mistyping analyses on any size of pedigree. |
| version | 2.91 |
| homepage | http://watson.hgen.pitt.edu/docs/simwalk2.html |
| commands | simwalk2 |
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| documentation |
http://bioweb2.pasteur.fr/docs/simwalk2/ |
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| description | It's a variant effect predictor tool, it predicts the effect of genetic variations (SNPs, insertions, deletions and MNPs) |
| version | 1.9 |
| homepage | http://snpeff.sourceforge.net/ |
| commands | snpEff-test |
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| description | It's a variant effect predictor tool, it predicts the effect of genetic variations (SNPs, insertions, deletions and MNPs) |
| version | 1.9 |
| homepage | http://snpeff.sourceforge.net/ |
| commands | snpEff |
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| description | SOLAR is a package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. |
| version | 4.1.5 |
| homepage | http://solar.sfbrgenetics.org/ |
| commands | solar |
| manpages | solar |
| documentation |
http://bioweb2.pasteur.fr/docs/solar/ |
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| description | tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples |
| version | 2.2.8 |
| homepage | http://varscan.sourceforge.net/ |
| commands | VarScan |
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