Jump to content

Mega2, the Manipulation Environment for Genetic Analysis: Difference between revisions

Add links
From Wikipedia, the free encyclopedia
Browse history interactively
← Previous editNext edit →
Content deleted Content added
VisualWikitext
Adding reference to new 2014 Mega2 paper.
Fixing the PubMed Central part of the Mega2 2014 paper reference, and citing the Mega2 2014 paper.
Line 38: Line 38:
}}
}}


'''Mega2, the Manipulation Environment for Genetic Analysis''', 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.<ref group=Mega2 name=Mega2_Abstract>{{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}}</ref><ref group=Mega2 name=Mega2_paper>{{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}}</ref><ref group=Mega2 name=Mega2_2013_Abstract>{{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}}</ref><ref group=Mega2 name=Mega2_2014_paper>{{cite journal | author=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 | pmid=PMC4269913 }}</ref> 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, the Manipulation Environment for Genetic Analysis''', 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.<ref group=Mega2 name=Mega2_Abstract>{{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}}</ref><ref group=Mega2 name=Mega2_paper>{{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}}</ref><ref group=Mega2 name=Mega2_2013_Abstract>{{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}}</ref><ref group=Mega2 name=Mega2_2014_paper>{{cite journal | author=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}}</ref> 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 has been used to facilitate genetic analyses of a wide variety of human traits, including hereditary dystonia,<ref>{{cite journal | author=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}}</ref> Ehlers-Danlos syndrome,<ref>{{cite journal | author=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}}</ref> multiple sclerosis,<ref>{{cite journal | author=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}}</ref> and gliomas.<ref>{{cite journal | author=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}}</ref> A list of PubMed Central articles citing Mega2 can be seen [http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&from_uid=15746282 here].
Mega2 has been used to facilitate genetic analyses of a wide variety of human traits, including hereditary dystonia,<ref>{{cite journal | author=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}}</ref> Ehlers-Danlos syndrome,<ref>{{cite journal | author=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}}</ref> multiple sclerosis,<ref>{{cite journal | author=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}}</ref> and gliomas.<ref>{{cite journal | author=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}}</ref> A list of PubMed Central articles citing Mega2 can be seen [http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&from_uid=15746282 here].
Line 55: Line 55:
|| 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]
|| 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]
|-
|-
| Mega2<ref group=Mega2 name=Mega2_Abstract /><ref group=Mega2 name=Mega2_paper /><ref group=Mega2 name=Mega2_2013_Abstract /> || simplified/augmented LINKAGE-format || [https://watson.hgen.pitt.edu/docs/mega2_html/mega2_documentation.html#sub:Annotated-file-formats Mega2 format]
| Mega2<ref group=Mega2 name=Mega2_Abstract /><ref group=Mega2 name=Mega2_paper /><ref group=Mega2 name=Mega2_2013_Abstract /><ref group=Mega2 name=Mega2_2014_paper /> || simplified/augmented LINKAGE-format || [https://watson.hgen.pitt.edu/docs/mega2_html/mega2_documentation.html#sub:Annotated-file-formats Mega2 format]
|-
|-
| PLINK<ref name=PLINK >{{cite journal | author=Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, 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}}</ref> || ped format or binary bed format || [http://pngu.mgh.harvard.edu/~purcell/plink/ PLINK documentation]
| PLINK<ref name=PLINK >{{cite journal | author=Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, 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}}</ref> || ped format or binary bed format || [http://pngu.mgh.harvard.edu/~purcell/plink/ PLINK documentation]
Line 104: Line 104:
|| [http://www.hgid.net/site/site.php?rubr=9# MLB-QTL]
|| [http://www.hgid.net/site/site.php?rubr=9# MLB-QTL]
|-
|-
| Mega2 annotated format<ref group=Mega2 name=Mega2_Abstract /><ref group=Mega2 name=Mega2_paper /><ref group=Mega2 name=Mega2_2013_Abstract /> || [https://watson.hgen.pitt.edu/docs/mega2_html/mega2_documentation.html#sub:Annotated-file-formats Mega2 format]
| Mega2 annotated format<ref group=Mega2 name=Mega2_Abstract /><ref group=Mega2 name=Mega2_paper /><ref group=Mega2 name=Mega2_2013_Abstract /><ref group=Mega2 name=Mega2_2014_paper /> || [https://watson.hgen.pitt.edu/docs/mega2_html/mega2_documentation.html#sub:Annotated-file-formats Mega2 format]
|-
|-
| Mendel format<ref name=MENDEL2013 >{{cite journal | author=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}}</ref>
| Mendel format<ref name=MENDEL2013 >{{cite journal | author=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}}</ref>

Revision as of 17:02, 26 March 2015

Mega2, the Manipulation Environment for Genetic Analysis
Original author(s)Previous Programmers: Charles P. Kollar, Nandita Mukhopadhyay, Lee Almasy, Mark Schroeder, William P. Mulvihill.
Developer(s)Daniel E. Weeks, Robert V. Baron.
Initial release2000
Stable release
4.7.1 / 2014
Repository
Written inC++
Operating systemLinux, Mac OS X, Microsoft Windows
TypeApplied statistical genetics, Bioinformatics
LicenseGNU General Public License Version 3
Websitewatson.hgen.pitt.edu/register/

Mega2, the Manipulation Environment for Genetic Analysis, 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.[Mega2 1][Mega2 2][Mega2 3][Mega2 4] 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 has been used to facilitate genetic analyses of a wide variety of human traits, including hereditary dystonia,[1] Ehlers-Danlos syndrome,[2] multiple sclerosis,[3] and gliomas.[4] A list of PubMed Central articles citing Mega2 can be seen 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.

Input format Description Links
LINKAGE[5][6][7][8] pre-Makeped or post-Makeped formats Linkage User Guide (PDF), LINKAGE format
Mega2[Mega2 1][Mega2 2][Mega2 3][Mega2 4] simplified/augmented LINKAGE-format Mega2 format
PLINK[9] ped format or binary bed format PLINK documentation
VCF or BCF Variant Call Format or Binary Variant Call Format Variant Call Format (Wikipedia entry), BCF documentation

Output file formats

Mega2 supports conversion to the following output formats.

Output format Links
ASPEX format ASPEX
Allegro format[10]
Beagle format[11][12] BEAGLE
CRANEFOOT format[13] CRANEFOOT
Eigenstrat format[14][15] EIGENSOFT
FBAT format[16] FBAT
GeneHunter format[17] GeneHunter
GeneHunter-Plus format[18] GeneHunter-Plus
IQLS/Idcoefs format[19][20] IQLS,Idcoefs
Linkage format[5][6][7][8] Linkage User Guide (PDF), LINKAGE format
Loki format[21] Loki
MLBQTL format[22] MLB-QTL
Mega2 annotated format[Mega2 1][Mega2 2][Mega2 3][Mega2 4] Mega2 format
Mendel format[23] Mendel
Merlin format[24] Merlin
Merlin/SimWalk2-NPL format[24][25] Merlin SimWalk2
PANGAEA MORGAN format[26][27] MORGAN
PAP format[28] PAP
PLINK format[9] (bed, lgen, or ped formats) PLINK
PREST format[29][30] PREST
PSEQ format PSEQ
Pre-makeped LINKAGE format[5][6][7][8] Linkage User Guide (PDF), LINKAGE format
SAGE format SAGE, openSAGE
SIMULATE format[31] SIMULATE
SLINK format[32][33] FASTSLINK
SOLAR format[34][35] SOLAR
SPLINK format[36] SPLINK
SUP format[33][37] SUP
SimWalk2 format[25] SimWalk2
Structure format[38][39][40] Structure
Vintage Mendel format[23][41] Vintage Mendel
Vitesse format[42] Vitesse

Mega2 documentation

The Mega2 documentation is available here in HTML format, and here in PDF format.

Download Mega2
Mega2 documentation (HTML)
Mega2 documentation (PDF)
Mega2 users Google Group
Mega2 bitbucket repository

References about Mega2

  1. ^ a b c Mukhopadhyay, N; Almasy L; Schroeder M; Mulvihill WP; Weeks DE (1999). "Mega2, a data-handling program for facilitating genetic linkage and association analyses". Am J Hum Genet. 65: A436.
  2. ^ a b c Mukhopadhyay, N; Almasy L; Schroeder M; Mulvihill WP; Weeks DE (2005). "Mega2: data-handling for facilitating genetic linkage and association analyses". Bioinformatics. 21 (10): 2556–2557. doi:10.1093/bioinformatics/bti364. PMID 15746282.
  3. ^ a b c Kollar, CP; Baron RV; Mukhopadhyay N; Weeks DE (October 2013). "Mega2: enhanced data-handling for facilitating genetic linkage and association analyses". Presented at the 63rd Annual Meeting of The American Society of Human Genetics, Boston: Abstract 1831.
  4. ^ a b c Baron RV, Kollar C, Mukhopadhyay N, Weeks DE (2014). "Mega2: validated data-reformatting for linkage and association analyses". Source Code Biol Med. 9 (1): 26. PMC 4269913.{{cite journal}}: CS1 maint: multiple names: authors list (link)

References

  1. ^ 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 (2013). "Mutations in the autoregulatory domain of beta-tubulin 4a cause hereditary dystonia". Ann Neurol. 73 (4): 546–553. doi:10.1002/ana.23832. PMC 3698699. PMID 23424103.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ 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 (2012). "Mutations in FKBP14 cause a variant of Ehlers-Danlos syndrome with progressive kyphoscoliosis, myopathy, and hearing loss". Am J Hum Genet. 90 (2): 201–216. doi:10.1016/j.ajhg.2011.12.004.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  3. ^ 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 (2012). "Exome sequencing identifies a novel multiple sclerosis susceptibility variant in the TYK2 gene". Neurology. 79 (5): 406–411. doi:10.1212/wnl.0b013e3182616fc4.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ 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 (2011). "Genome-wide high-density SNP linkage search for glioma susceptibility loci: results from the Gliogene Consortium". Cancer Res. 71 (24): 7568–7575. doi:10.1158/0008-5472.can-11-0013.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  5. ^ a b c Lathrop GM, Lalouel J-M (1984). "Easy calculations of lod scores and genetic risks on small computers". Am J Hum Genet. 36: 460–465.
  6. ^ a b c Lathrop GM, Lalouel JM, Julier C, Ott J (1985). "Multilocus linkage analysis in humans: detection of linkage and estimation of recombination". Am J Hum Genet. 37 (3): 482–498.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  7. ^ a b c Lathrop GM, Lalouel JM, White RL (1986). "Construction of human linkage maps: likelihood calculations for multilocus analysis". Genet Epidemiol. 3: 39–52. doi:10.1002/gepi.1370030105.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  8. ^ a b c Lathrop GM, Lalouel JM (1988). "Efficient computations in multilocus linkage analysis". Am J Hum Genet. 42: 498–505.
  9. ^ Gudbjartsson DF, Jonasson K, Frigge ML, Kong A (2000). "Allegro, a new computer program for multipoint linkage analysis". Nat Genet. 25 (1): 12–13. doi:10.1038/75514.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  10. ^ Browning SR, Browning BL (2007). "Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering". Am J Hum Genet. 81 (5): 1084–1097. doi:10.1086/521987. PMC 2265661. PMID 17924348.
  11. ^ Browning BL, Browning SR (2009). "A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals". Am J Hum Genet. 84 (2): 210–223. doi:10.1016/j.ajhg.2009.01.005. PMC 2668004. PMID 19200528.
  12. ^ Makinen VP, Parkkonen M, Wessman M, Groop PH, Kanninen T, Kaski K (2005). "High-throughput pedigree drawing". Eur J Hum Genet. 13 (8): 987–989. doi:10.1038/sj.ejhg.5201430.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  13. ^ Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006). "Principal components analysis corrects for stratification in genome-wide association studies". Nat Genet. 38 (8): 904–909. doi:10.1038/ng1847. PMID 16862161.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  14. ^ Patterson N, Price AL, Reich D (2006). "Population structure and eigenanalysis". PLoS Genet. 2 (12): e190. doi:10.1371/journal.pgen.0020190. PMC 1713260. PMID 17194218.{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  15. ^ Laird NM, Horvath S, Xu X (2000). "Implementing a unified approach to family-based tests of association". Genet Epidemiol. 19 (Suppl 1): S36-42. doi:10.1002/1098-2272(2000)19:1+<::aid-gepi6>3.3.co;2-d.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  16. ^ Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES (1996). "Parametric and nonparametric linkage analysis: a unified multipoint approach". Am J Hum Genet. 58: 1347–1363.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  17. ^ Kong A, Cox NJ (1997). "Allele-sharing models: LOD scores and accurate linkage tests". Am J Hum Genet. 61 (5): 1179–1188. doi:10.1086/301592.
  18. ^ Wang Z, McPeek MS (2009). "An Incomplete-Data Quasi-likelihood Approach to Haplotype-Based Genetic Association Studies on Related Individuals". J Am Stat Assoc. 104 (487): 1251–1260. doi:10.1198/jasa.2009.tm08507.
  19. ^ Abney M (2009). "A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients". Bioinformatics. 25 (12): 1561–1563. doi:10.1093/bioinformatics/btp185.
  20. ^ Heath SC (1997). "Markov chain Monte Carlo segregation and linkage analysis for oligogenic models". Am J Hum Genet. 61 (3): 748–760. doi:10.1086/515506.
  21. ^ Alcais A, Philippi A, Abel L (1999). "Genetic model-free linkage analysis using the maximum-likelihood- binomial method for categorical traits". Genet Epidemiol. 17 (Suppl 1): S467-472. doi:10.1002/gepi.1370170775.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  22. ^ a b Lange K, Papp JC, Sinsheimer JS, Sripracha R, Zhou H, Sobel EM (2013). "Mendel: the Swiss army knife of genetic analysis programs". Bioinformatics. 29 (12): 1568–1570. doi:10.1093/bioinformatics/btt187.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  23. ^ a b Abecasis GR, Cherny SS, Cookson WO, Cardon LR (2002). "Merlin--rapid analysis of dense genetic maps using sparse gene flow trees". Nat Genet. 30 (1): 97–101. doi:10.1038/ng786. PMID 11731797.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  24. ^ a b Sobel E, Lange K (1996). "Descent graphs in pedigree analysis: Applications to haplotyping, location scores, and marker-sharing statistics". Am J Hum Genet. 58 (6): 1323–1337.
  25. ^ Thompson EA (1994). "Monte Carlo likelihood in the genetic mapping of complex traits". Philos Trans R Soc Lond B Biol Sci. 344 (1310): 345–350, discussion 350–341. doi:10.1098/rstb.1994.0073.
  26. ^ Thompson EA (1994). "Monte Carlo likelihood in genetic mapping". Statistical Science. 9 (3): 355–366. doi:10.1214/ss/1177010381.
  27. ^ Hasstedt SJ (2005). "jPAP: Document-driven software for genetic analysis". Genet Epidemiol. 29: 255.
  28. ^ McPeek MS, Sun L (2000). "Statistical tests for detection of misspecified relationships by use of genome-screen data". Am J Hum Genet. 66 (3): 1076–1094. doi:10.1086/302800.
  29. ^ Sun L, Wilder K, McPeek MS (2002). "Enhanced pedigree error detection". Hum Hered. 54 (2): 99–110. doi:10.1159/000067666. PMID 12566741.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  30. ^ Speer M, Terwilliger JD, Ott J (1992). "A chromosome-based method for rapid computer simulation". Am J Hum Genet. 51: A202.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  31. ^ Weeks DE, Ott J, Lathrop GM (1990). "SLINK: a general simulation program for linkage analysis". Am J Hum Genet. 47 (3): A204.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  32. ^ Blangero J, Almasy L (1997). "Multipoint oligogenic linkage analysis of quantitative traits". Genet Epidemiol. 14 (6): 959–964. doi:10.1002/(sici)1098-2272(1997)14:6<959::aid-gepi66>3.0.co;2-k.
  33. ^ Almasy L, Blangero J (1998). "Multipoint quantitative-trait linkage analysis in general pedigrees". Am J Hum Genet. 62 (5): 1198–1211. doi:10.1086/301844.
  34. ^ Holmans P (1993). "Asymptotic properties of affected-sib-pair linkage analysis". Am J Hum Genet. 52 (2): 362–374.
  35. ^ Lemire M (2006). "SUP: an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values". BMC Genet. 7: 40.
  36. ^ Pritchard JK, Stephens M, Donnelly P (2000). "Inference of population structure using multilocus genotype data". Genetics. 155 (2): 945–959. PMC 1461096. PMID 10835412.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  37. ^ Falush D, Stephens M, Pritchard JK (2003). "Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies". Genetics. 164 (4): 1567–1587.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  38. ^ Falush D, Stephens M, Pritchard JK (2007). "Inference of population structure using multilocus genotype data: dominant markers and null alleles". Mol Ecol Notes. 7 (4): 574–578. doi:10.1111/j.1471-8286.2007.01758.x.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  39. ^ Lange K, Weeks D, Boehnke M (1988). "Programs for pedigree analysis: MENDEL, FISHER, and dGENE". Genet Epidemiol. 5: 471–472. doi:10.1002/gepi.1370050611.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  40. ^ O'Connell JR, Weeks DE (1995). "The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance". Nat Genet. 11 (4): 402–408. doi:10.1038/ng1295-402.
Retrieved from "https://en.wikipedia.org/w/index.php?title=Mega2,_the_Manipulation_Environment_for_Genetic_Analysis&oldid=653627772"