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Mega2, the Manipulation Environment for Genetic Analysis

{{Infobox software

| name = Mega2

| logo =

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| author = Previous Programmers: Charles P. Kollar, Nandita Mukhopadhyay, Lee Almasy, Mark Schroeder, William P. Mulvihill.

| developer = Daniel E. Weeks, Robert V. Baron, Justin R. Stickel.

| released = {{Start date and age|2000|1|16|df=yes}}

| discontinued =

| latest release version = 5.0.1

| latest release date = {{Start date and age|2018|12|13|df=yes}}

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| programming language = C++

| operating system = Linux, Mac OS X, Microsoft Windows

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| genre = Applied statistical genetics, Bioinformatics

| license = GNU General Public License version 3

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| website = {{URL|https://watson.hgen.pitt.edu/register/}}

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Mega2 is a data manipulation software for applied statistical genetics. Mega is an acronym for Manipulation Environment for Genetic Analysis.

The software allows the applied statistical geneticist to convert one's data from several input formats to a large number output formats suitable for analysis by commonly used software packages.{{cite journal|last=Mukhopadhyay|first=N|author2=Almasy L |author3=Schroeder M |author4=Mulvihill WP |author5=Weeks DE |title=Mega2, a data-handling program for facilitating genetic linkage and association analyses|journal=Am J Hum Genet|date=1999|volume=65|page=A436}}{{cite journal|last=Mukhopadhyay|first=N|author2=Almasy L |author3=Schroeder M |author4=Mulvihill WP |author5=Weeks DE |title=Mega2: data-handling for facilitating genetic linkage and association analyses|journal=Bioinformatics|date=2005|volume=21|issue=10|pages=2556–2557|pmid=15746282 |doi=10.1093/bioinformatics/bti364|doi-access=free}}{{cite journal|last=Kollar|first=CP|author2=Baron RV |author3=Mukhopadhyay N |author4=Weeks DE |title=Mega2: enhanced data-handling for facilitating genetic linkage and association analyses|journal=Presented at the 63rd Annual Meeting of the American Society of Human Genetics, Boston|date=October 2013|page=Abstract 1831|url=http://abstracts.ashg.org/cgi-bin/2013/ashg13s.pl?author=kollar&sort=ptimes&sbutton=Detail&absno=130121140&sid=32111}}{{cite journal |vauthors=Baron RV, Kollar C, Mukhopadhyay N, Weeks DE | title=Mega2: validated data-reformatting for linkage and association analyses | journal=Source Code Biol Med | date=2014 | volume=9 | issue=1|pages=26|pmc=4269913 | doi=10.1186/s13029-014-0026-y | pmid=25687422 | doi-access=free }} In a typical human genetics study, the analyst often needs to use a variety of different software programs to analyze the data, and these programs usually require that the data be formatted to their precise input specifications. Conversion of one's data into these multiple different formats can be tedious, time-consuming, and error-prone. Mega2, by providing validated conversion pipelines, can accelerate the analyses while reducing errors.

Mega2 produces a common intermediate data representation using SQLite3, which enables the data to be accessed by other programs and languages. In particular, the [https://cran.r-project.org/package=Mega2R Mega2R] R package converts the SQLite3 data into R data frames. Several R functions are provided that illustrate how data can be extracted from the data frames for common R analysis, such as [https://cran.r-project.org/package=SKAT SKAT] and [https://cran.r-project.org/package=pedgene pedgene]. The key is being able to efficiently extract genotypes corresponding to chosen subsets of markers so as to facilitate gene-based association testing by automating looping over genes in the genome. Another function converts to VCF format and another converts the data to [https://cran.r-project.org/package=GenABEL GenABEL] format. For more information about the Mega2R package, see [https://watson.hgen.pitt.edu/mega2/mega2r/ here].

Mega2 has been used to facilitate genetic analyses of a wide variety of human traits, including hereditary dystonia,{{cite journal |vauthors=Hersheson J, Mencacci NE, Davis M, Macdonald N, Trabzuni D, Ryten M, Pittman A, Paudel R, Kara E, Fawcett K, Plagnol V, Bhatia KP, Medlar AJ, Stanescu HC, Hardy J, Kleta R, Wood NW, Houlden H | title=Mutations in the autoregulatory domain of beta-tubulin 4a cause hereditary dystonia | journal=Ann Neurol | date=2013 | volume=73 | issue=4|pages=546–553 | doi=10.1002/ana.23832 | pmid=23424103 | pmc=3698699}} Ehlers-Danlos syndrome,{{cite journal |vauthors=Baumann M, Giunta C, Krabichler B, Ruschendorf F, Zoppi N, Colombi M, Bittner RE, Quijano-Roy S, Muntoni F, Cirak S, Schreiber G, Zou Y, Hu Y, Romero NB, Carlier RY, Amberger A, Deutschmann A, Straub V, Rohrbach M, Steinmann B, Rostasy K, Karall D, Bonnemann CG, Zschocke J, Fauth C | title=Mutations in FKBP14 cause a variant of Ehlers-Danlos syndrome with progressive kyphoscoliosis, myopathy, and hearing loss | journal=Am J Hum Genet | date=2012 | volume=90 | issue=2|pages=201–216 | doi=10.1016/j.ajhg.2011.12.004 | pmid=22265013 | pmc=3276673}} multiple sclerosis,{{cite journal |vauthors=Dyment DA, Cader MZ, Chao MJ, Lincoln MR, Morrison KM, Disanto G, Morahan JM, De Luca GC, Sadovnick AD, Lepage P, Montpetit A, Ebers GC, Ramagopalan SV | title=Exome sequencing identifies a novel multiple sclerosis susceptibility variant in the TYK2 gene | journal=Neurology | date=2012 | volume=79 | issue=5|pages=406–411 | doi=10.1212/wnl.0b013e3182616fc4 | pmid=22744673 | pmc=3405256}} and gliomas.{{cite journal |vauthors=Shete S, Lau CC, Houlston RS, Claus EB, Barnholtz-Sloan J, Lai R, Il'yasova D, Schildkraut J, Sadetzki S, Johansen C, Bernstein JL, Olson SH, Jenkins RB, Yang P, Vick NA, Wrensch M, Davis FG, McCarthy BJ, Leung EH, Davis C, Cheng R, Hosking FJ, Armstrong GN, Liu Y, Yu RK, Henriksson R, Gliogene C, Melin BS, Bondy ML | title=Genome-wide high-density SNP linkage search for glioma susceptibility loci: results from the Gliogene Consortium | journal=Cancer Res | date=2011 | volume=71 | issue=24|pages=7568–7575 | doi=10.1158/0008-5472.can-11-0013 | pmid=22037877 | pmc=3242820}} A list of PubMed Central articles citing Mega2 can be seen [https://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&from_uid=15746282 here].

Mega2, which focusses on data reformatting, should not be confused with the MEGA, Molecular Evolutionary Genetics Analysis program, which focuses on molecular evolution and phylogenetics.

Input file formats

Mega2 accepts input data in a variety of widely used file formats. These contain, at a minimum, data about the phenotypes, the marker genotypes, any family structures, and map positions of the markers.

class="wikitable"
Input formatDescriptionLinks
LINKAGE{{cite journal |vauthors=Lathrop GM, Lalouel JM | title=Easy calculations of lod scores and genetic risks on small computers | journal=Am J Hum Genet | date=1984 | volume=36 | issue=2 |pages=460–465 | pmc=1684427 | pmid=6585139 }}{{cite journal |vauthors=Lathrop GM, Lalouel JM, Julier C, Ott J | title=Multilocus linkage analysis in humans: detection of linkage and estimation of recombination | journal=Am J Hum Genet | date=1985 | volume=37 | issue=3|pages=482–498 | pmc=1684598 | pmid=3859205 }}{{cite journal |vauthors=Lathrop GM, Lalouel JM, White RL | title=Construction of human linkage maps: likelihood calculations for multilocus analysis | journal=Genet Epidemiol | date=1986 | volume=3 | issue=1 |pages=39–52 | doi=10.1002/gepi.1370030105| pmid=3957003 | s2cid=29289413 }}{{cite journal |vauthors=Lathrop GM, Lalouel JM | title=Efficient computations in multilocus linkage analysis | journal=Am J Hum Genet | date=1988 | volume=42 | issue=3 |pages=498–505 | pmid=3162348 | pmc=1715153 }}pre-Makeped or post-Makeped formats[http://www.jurgott.org/linkage/LinkageUser.pdf Linkage User Guide (PDF)], [https://watson.hgen.pitt.edu/docs/mega2_html/mega2_documentation.html#sub:Linkage-file-formats LINKAGE format]
Mega2simplified/augmented LINKAGE-format[https://watson.hgen.pitt.edu/docs/mega2_html/mega2_documentation.html#sub:Annotated-file-formats Mega2 format]
PLINK{{cite journal |vauthors=Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC | title=PLINK: a tool set for whole-genome association and population-based linkage analyses | journal=Am J Hum Genet | date=2007 | volume=81 | issue=3|pages=559–575 | pmid=17701901 | doi=10.1086/519795 | pmc=1950838}}ped format or binary bed format[https://web.archive.org/web/20081207192023/http://pngu.mgh.harvard.edu/~purcell/plink/ PLINK documentation]
VCF or BCF{{cite journal |vauthors=Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, etal | title=The variant call format and VCFtools. | journal=Bioinformatics | year= 2011 | volume= 27 | issue= 15 | pages= 2156–8 | pmid=21653522 | doi=10.1093/bioinformatics/btr330 | pmc=3137218 }}Variant Call Format or Binary Variant Call FormatVariant Call Format (Wikipedia entry), [http://www.1000genomes.org/wiki/analysis/variant-call-format/bcf-binary-vcf-version-2 BCF documentation]
IMPUTE2{{cite journal |vauthors=Howie BN, Donnelly P, Marchini J | title=A flexible and accurate genotype imputation method for the next generation of genome-wide association studies | journal=PLOS Genet | date=2009 | volume=5 | issue=6|pages=e1000529|pmc= 2689936 | doi=10.1371/journal.pgen.1000529 | pmid=19543373 | doi-access=free }}{{cite journal |vauthors=Marchini J, Howie B | title=Genotype imputation for genome-wide association studies | journal=Nat Rev Genet | date=2010 | volume=11 | issue=7|pages=499–511|pmid= 20517342 | doi=10.1038/nrg2796| s2cid=1465707 }}IMPUTE2 GEN and BGEN Formats[https://mathgen.stats.ox.ac.uk/impute/impute_v2.html IMPUTE2 documentation], [http://www.stats.ox.ac.uk/%7Emarchini/software/gwas/file_format.html GEN format], [http://www.well.ox.ac.uk/~gav/bgen_format/bgen_format.html BGEN format]

Output file formats

Mega2 supports conversion to the following output formats.

class="wikitable"
Output formatLinks
ASPEX format[http://aspex.sourceforge.net ASPEX]
Allegro format{{cite journal |vauthors=Gudbjartsson DF, Jonasson K, Frigge ML, Kong A | title=Allegro, a new computer program for multipoint linkage analysis | journal=Nat Genet | date=2000 | volume=25 | issue=1|pages=12–13 | doi=10.1038/75514| pmid=10802644 | s2cid=27362146 }}
Beagle format{{cite journal |vauthors=Browning SR, Browning BL | title=Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering | journal=Am J Hum Genet | date=2007 | volume=81 | issue=5|pages=1084–1097 | doi=10.1086/521987 | pmid=17924348 | pmc=2265661}}{{cite journal |vauthors=Browning BL, Browning SR | title=A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals | journal=Am J Hum Genet | date=2009 | volume=84 | issue=2|pages=210–223 | pmid=19200528 | doi=10.1016/j.ajhg.2009.01.005 | pmc=2668004}}[http://faculty.washington.edu/browning/beagle/beagle.html BEAGLE]
CRANEFOOT format{{cite journal |vauthors=Makinen VP, Parkkonen M, Wessman M, Groop PH, Kanninen T, Kaski K | title=High-throughput pedigree drawing | journal=Eur J Hum Genet | date=2005 | volume=13 | issue=8|pages=987–989 | doi=10.1038/sj.ejhg.5201430| pmid=15870825 | doi-access=free }}[http://www.finndiane.fi/software/cranefoot/ CRANEFOOT]
Eigenstrat format{{cite journal |vauthors=Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D | title=Principal components analysis corrects for stratification in genome-wide association studies | journal=Nat Genet | date=2006 | volume=38 | issue=8|pages=904–909 | doi=10.1038/ng1847 | pmid=16862161| s2cid=8127858 }}{{cite journal |vauthors=Patterson N, Price AL, Reich D | title=Population structure and eigenanalysis | journal=PLOS Genet | date=2006 | volume=2 | issue=12|pages=e190 | doi=10.1371/journal.pgen.0020190 | pmid=17194218 | pmc=1713260 | doi-access=free }}[http://www.hsph.harvard.edu/alkes-price/software/ EIGENSOFT]
FBAT format{{cite journal |vauthors=Laird NM, Horvath S, Xu X | title=Implementing a unified approach to family-based tests of association | journal=Genet Epidemiol | date=2000 | volume=19 | issue=Suppl 1|pages=S36–42 | doi=10.1002/1098-2272(2000)19:1+<::aid-gepi6>3.3.co;2-d| pmid=11055368 }}[http://www.hsph.harvard.edu/fbat/fbat.htm FBAT]
GeneHunter format{{cite journal |vauthors=Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES | title=Parametric and nonparametric linkage analysis: a unified multipoint approach | journal=Am J Hum Genet | date=1996 | volume=58 | issue=6 |pages=1347–1363 | pmid=8651312 | pmc=1915045 }}[http://www.broadinstitute.org/ftp/distribution/software/genehunter/ GeneHunter]
GeneHunter-Plus format{{cite journal |vauthors=Kong A, Cox NJ | title=Allele-sharing models: LOD scores and accurate linkage tests | journal=Am J Hum Genet | date=1997 | volume=61 | issue=5|pages=1179–1188 | doi=10.1086/301592| pmid=9345087 | pmc=1716027 }}[http://galton.uchicago.edu/genehunterplus/ GeneHunter-Plus]
IQLS/Idcoefs format{{cite journal |vauthors=Wang Z, McPeek MS | title=An Incomplete-Data Quasi-likelihood Approach to Haplotype-Based Genetic Association Studies on Related Individuals | journal=J Am Stat Assoc | date=2009 | volume=104 | issue=487|pages=1251–1260 | doi=10.1198/jasa.2009.tm08507| pmid=20428335 | pmc=2860453 }}{{cite journal | author=Abney M | title=A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients | journal=Bioinformatics | date=2009 | volume=25 | issue=12|pages=1561–1563 | doi=10.1093/bioinformatics/btp185 | pmid=19359355 | pmc=2687941}}[http://www.stat.uchicago.edu/~mcpeek/software/IQLS/index.html IQLS],[http://home.uchicago.edu/~abney/abney_web/Software.html Idcoefs]
Linkage format[http://www.jurgott.org/linkage/LinkageUser.pdf Linkage User Guide (PDF)], [https://watson.hgen.pitt.edu/docs/mega2_html/mega2_documentation.html#sub:Linkage-file-formats LINKAGE format]
Loki format{{cite journal | author=Heath SC | title=Markov chain Monte Carlo segregation and linkage analysis for oligogenic models | journal=Am J Hum Genet | date=1997 | volume=61 | issue=3|pages=748–760 | doi=10.1086/515506| pmid=9326339 | pmc=1715966 }}[https://www.stat.washington.edu/thompson/Genepi/Loki.shtml Loki]
MaCH/minimac3 format{{cite journal |vauthors=Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR | title=Fast and accurate genotype imputation in genome-wide association studies through pre-phasing | journal=Nat Genet | date=2012 | volume=44 | issue=8|pages=955–959 | doi=10.1038/ng.2354 | pmid=22820512 | pmc=3696580}} {{cite journal |vauthors=Fuchsberger C, Abecasis GR, Hinds DA | title=minimac2: faster genotype imputation | journal=Bioinformatics | date=2015 | volume=31 | issue=5|pages=782–784 | doi=10.1093/bioinformatics/btu704 | pmid=25338720 | pmc=4341061}}[http://csg.sph.umich.edu//abecasis/MACH/index.html MaCH], [http://genome.sph.umich.edu/wiki/Minimac3 minimac3]
MLBQTL format{{cite journal |vauthors=Alcais A, Philippi A, Abel L | title=Genetic model-free linkage analysis using the maximum-likelihood- binomial method for categorical traits | journal=Genet Epidemiol | date=1999 | volume=17 | issue=Suppl 1|pages=S467–472 | doi=10.1002/gepi.1370170775| pmid=10597477 | doi-access=free }}[http://www.hgid.net/site/site.php?rubr=9# MLB-QTL]
Mega2 annotated format[https://watson.hgen.pitt.edu/docs/mega2_html/mega2_documentation.html#sub:Annotated-file-formats Mega2 format]
Mendel format{{cite journal |vauthors=Lange K, Papp JC, Sinsheimer JS, Sripracha R, Zhou H, Sobel EM | title=Mendel: the Swiss army knife of genetic analysis programs | journal=Bioinformatics | date=2013 | volume=29 | issue=12|pages=1568–1570 | doi=10.1093/bioinformatics/btt187 | pmid=23610370 | pmc=3673222}}[http://www.genetics.ucla.edu/software/ Mendel]
Merlin format{{cite journal |vauthors=Abecasis GR, Cherny SS, Cookson WO, Cardon LR | title=Merlin--rapid analysis of dense genetic maps using sparse gene flow trees | journal=Nat Genet | date=2002 | volume=30 | issue=1|pages=97–101 | doi=10.1038/ng786 | pmid=11731797| s2cid=12226524 }}[http://www.sph.umich.edu/csg/abecasis/Merlin Merlin]
Merlin/SimWalk2-NPL format[http://www.sph.umich.edu/csg/abecasis/Merlin Merlin] [https://watson.hgen.pitt.edu/register SimWalk2]
PANGAEA MORGAN format{{cite journal | author=Thompson EA | title=Monte Carlo likelihood in the genetic mapping of complex traits | journal=Philos Trans R Soc Lond B Biol Sci | date=1994 | volume=344 | issue=1310|pages=345–350; discussion 350–341 | doi = 10.1098/rstb.1994.0073 | pmid=7800704 }}{{cite journal | author=Thompson EA | title=Monte Carlo likelihood in genetic mapping | journal=Statistical Science | date=1994 | volume=9 | issue=3|pages=355–366 | doi=10.1214/ss/1177010381| doi-access=free }}[http://www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.shtml MORGAN]
PAP format{{cite journal | author=Hasstedt SJ | title=jPAP: Document-driven software for genetic analysis | journal=Genet Epidemiol | date=2005 | volume=29 |pages=255 }}[http://hasstedt.genetics.utah.edu/ PAP]
PLINK format (bed, lgen, or ped formats)[https://web.archive.org/web/20081207192023/http://pngu.mgh.harvard.edu/~purcell/plink/ PLINK]
PREST format{{cite journal |vauthors=McPeek MS, Sun L | title=Statistical tests for detection of misspecified relationships by use of genome-screen data | journal=Am J Hum Genet | date=2000 | volume=66 | issue=3|pages=1076–1094 | doi=10.1086/302800 | pmid=10712219 | pmc=1288143}}{{cite journal |vauthors=Sun L, Wilder K, McPeek MS | title=Enhanced pedigree error detection | journal=Hum Hered | date=2002 | volume=54 | issue=2|pages=99–110 | doi=10.1159/000067666 | pmid=12566741| s2cid=26992288 }}[http://fisher.utstat.toronto.edu/sun/Software/Prest/prest3.02/index.html PREST]
PSEQ format[https://web.archive.org/web/20140723030328/http://atgu.mgh.harvard.edu/plinkseq/ PSEQ]
Pre-makeped LINKAGE format[http://www.jurgott.org/linkage/LinkageUser.pdf Linkage User Guide (PDF)], [https://watson.hgen.pitt.edu/docs/mega2_html/mega2_documentation.html#sub:Linkage-file-formats LINKAGE format]
ROADTRIPS format{{cite journal |vauthors=Thornton T, McPeek MS | title=ROADTRIPS: case-control association testing with partially or completely unknown population and pedigree structure | journal=Am J Hum Genet | date=2010 | volume=86 | issue=2|pages=172–184 | doi=10.1016/j.ajhg.2010.01.001 | pmid=20137780 | pmc=2820184}}[http://faculty.washington.edu/tathornt/software/ROADTRIPS2/ ROADTRIPS]
SAGE format[http://darwin.cwru.edu/ SAGE], [http://code.google.com/p/opensage/ openSAGE]
SHAPEIT format{{cite journal|vauthors=Delaneau O, Marchini J, Zagury JF | title=A linear complexity phasing method for thousands of genomes. | journal=Nat Methods | year= 2012 | volume= 9 | issue= 2 | pages= 179–81 | pmid=22138821 | doi=10.1038/nmeth.1785 | s2cid=13765612 }}{{cite journal|vauthors=Delaneau O, Zagury JF, Marchini J | title=Improved whole-chromosome phasing for disease and population genetic studies. | journal=Nat Methods | year= 2013 | volume= 10 | issue= 1 | pages= 5–6 | pmid=23269371 | doi=10.1038/nmeth.2307 | s2cid=205421216 }}{{cite journal|vauthors=Delaneau O, Howie B, Cox AJ, Zagury JF, Marchini J | title=Haplotype estimation using sequencing reads. | journal=Am J Hum Genet | year= 2013 | volume= 93 | issue= 4 | pages= 687–96 | pmid=24094745 | doi=10.1016/j.ajhg.2013.09.002 | pmc=3791270 }}{{cite journal|vauthors=O'Connell J, Gurdasani D, Delaneau O, Pirastu N, Ulivi S, Cocca M | title=A general approach for haplotype phasing across the full spectrum of relatedness. | journal=PLOS Genet | year= 2014 | volume= 10 | issue= 4 | pages= e1004234 | pmid=24743097 | doi=10.1371/journal.pgen.1004234 | pmc=3990520 |display-authors=etal | doi-access=free }}{{cite journal |vauthors=Delaneau O, Marchini J, ((The 1000 Genomes Project Consortium)) |title=Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel | journal=Nat Commun | year= 2014 | volume= 5 | pages= 3934 | pmid=25653097 | doi=10.1038/ncomms4934 | pmc=4338501 |bibcode=2014NatCo...5.3934. }}[https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html SHAPEIT]
SIMULATE format{{cite journal |vauthors=Speer M, Terwilliger JD, Ott J | title=A chromosome-based method for rapid computer simulation | journal=Am J Hum Genet | date=1992 | volume=51 |pages=A202 }}[http://www.jurgott.org/linkage/simulate.html SIMULATE]
SLINK format{{cite journal |vauthors=Weeks DE, Ott J, Lathrop GM | title=SLINK: a general simulation program for linkage analysis | journal=Am J Hum Genet | date=1990 | volume=47 | issue=3|pages=A204 }}{{cite journal |vauthors=Schäffer AA, Lemire M, Ott J, Lathrop GM, Weeks DE | title=Coordinated conditional simulation with SLINK and SUP of many markers linked or associated to a trait in large pedigrees | journal=Hum Hered | date=2011 | volume=71 | issue=2|pages=126–134 | pmid=21734403 | doi=10.1159/000324177 | pmc=3136384}}[https://watson.hgen.pitt.edu/register FASTSLINK]
SOLAR format{{cite journal |vauthors=Blangero J, Almasy L | title=Multipoint oligogenic linkage analysis of quantitative traits | journal=Genet Epidemiol | date=1997 | volume=14 | issue=6|pages=959–964 | doi=10.1002/(sici)1098-2272(1997)14:6<959::aid-gepi66>3.0.co;2-k| pmid=9433607 | s2cid=11630296 }}{{cite journal |vauthors=Almasy L, Blangero J | title=Multipoint quantitative-trait linkage analysis in general pedigrees | journal=Am J Hum Genet | date=1998 | volume=62 | issue=5|pages=1198–1211 | doi=10.1086/301844| pmid=9545414 | pmc=1377101 }}[http://solar.txbiomedgenetics.org/download.html SOLAR]
SPLINK format{{cite journal | author=Holmans P | title=Asymptotic properties of affected-sib-pair linkage analysis | journal=Am J Hum Genet | date=1993 | volume=52 | issue=2|pages=362–374 | pmid=8430697 | pmc=1682211 }}[https://web.archive.org/web/20070726120937/http://www-gene.cimr.cam.ac.uk/clayton/software/ SPLINK]
SUP format{{cite journal | author=Lemire M | title=SUP: an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values | journal=BMC Genet | date=2006 | volume=7 |pages=40 | doi=10.1186/1471-2156-7-40 | pmid=16803631 | pmc=1524809 | doi-access=free }}[http://mlemire.freeshell.org/software.html SUP]
SimWalk2 format{{cite journal |vauthors=Sobel E, Lange K | title=Descent graphs in pedigree analysis: Applications to haplotyping, location scores, and marker-sharing statistics | journal=Am J Hum Genet | date=1996 | volume=58 | issue=6|pages=1323–1337 | pmid=8651310 | pmc=1915074 }}[https://watson.hgen.pitt.edu/register SimWalk2]
Structure format{{cite journal |vauthors=Pritchard JK, Stephens M, Donnelly P | title=Inference of population structure using multilocus genotype data | journal=Genetics | date=2000 | volume=155 | issue=2|pages=945–959 | doi=10.1093/genetics/155.2.945 | pmid=10835412 | pmc=1461096}}{{cite journal |vauthors=Falush D, Stephens M, Pritchard JK | title=Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies | journal=Genetics | date=2003 | volume=164 | issue=4|pages=1567–1587 | doi=10.1093/genetics/164.4.1567 | pmid=12930761 | pmc=1462648 }}{{cite journal |vauthors=Falush D, Stephens M, Pritchard JK | title=Inference of population structure using multilocus genotype data: dominant markers and null alleles | journal=Mol Ecol Notes | date=2007 | volume=7 | issue=4|pages=574–578 | doi=10.1111/j.1471-8286.2007.01758.x| pmid=18784791 | pmc=1974779 }}[https://web.archive.org/web/20131219061524/http://pritchardlab.stanford.edu/structure.html Structure]
VCF formatVariant Call Format (Wikipedia entry)
Vintage Mendel format{{cite journal |vauthors=Lange K, Weeks D, Boehnke M | title=Programs for pedigree analysis: MENDEL, FISHER, and dGENE | journal=Genet Epidemiol | date=1988 | volume=5 | issue=6 |pages=471–472 | doi=10.1002/gepi.1370050611| pmid=3061869 | url=https://deepblue.lib.umich.edu/bitstream/2027.42/101847/1/1370050611_ftp.pdf | hdl=2027.42/101847 | s2cid=44260724 | hdl-access=free }}[http://www.genetics.ucla.edu/software/ Vintage Mendel]
Vitesse format{{cite journal |vauthors=O'Connell JR, Weeks DE | title=The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance | journal=Nat Genet | date=1995 | volume=11 |pages=402–408 | doi=10.1038/ng1295-402 | issue=4 | pmid=7493020| s2cid=12496754 }}[https://watson.hgen.pitt.edu/register Vitesse]

Documentation

The Mega2 documentation is available [https://watson.hgen.pitt.edu/docs/mega2_html/mega2.html here] in HTML format, and [https://watson.hgen.pitt.edu/docs/mega2_html/Mega2_Documentation.pdf here] in PDF format.

References

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External links

  • [https://watson.hgen.pitt.edu/register Download Mega2]
  • [https://watson.hgen.pitt.edu/docs/mega2_html/mega2.html Mega2 documentation (HTML)]
  • [https://watson.hgen.pitt.edu/docs/mega2_html/Mega2_Documentation.pdf Mega2 documentation (PDF)]
  • [https://groups.google.com/forum/#!forum/mega2-users Mega2 users Google Group]
  • [https://bitbucket.org/dweeks/mega2 Mega2 bitbucket repository]
  • [https://watson.hgen.pitt.edu/mega2/mega2r/ The Mega2R R package]

Category:Free bioinformatics software