Multiplex Manager

Streamline Your Design

Screen Shots
Screen Shots  


The following short technical report has been accepted by BioTechniques and is available online:

Holleley CE and Geerts PG ( 2009 ) Multiplex Manager 1.0: a crossplatform computer program that plans and optimizes multiplex PCR
BioTechniques, Vol 46, No 7, pp 511-517

Supplementary Materials

The paper refers to the Marshfield Clinic screening sets:

You can download The Marshfield Data Set as a Multiplex Manager input file for Set 12 here: MarshfieldSet12.xml.

View a sample report generated for the The Marshfield Data Set here: Set 12 Report

This file was generated using the Import CSV Data option in the Utilities menu.

Sample File used in the Screencast: Sample Input File.xml.

Studies that have used Multiplex Manager

  1. A parentage study using microsatellite loci in a pilot project for aquaculture of the European anchovy Engraulis encrasicolus L.
    Aquaculture 310 305-311   DOI:16/j.aquaculture.2010.10.025
    Yaisel J. Borrell, Jorge Alvarez, Gloria Blanco, Amalia Mártinez De Murguía, Deborah Lee, Carlos Fernández, Concha Martínez, Unai Cotano, Paula álvarez, José Antonio Sanchez Prado

  2. Assessment of parental contributions to fast- and slow-growing progenies in the sea bream Sparus aurata L. using a new multiplex PCR
    Aquaculture 314 58-65   DOI:16/j.aquaculture.2011.01.028
    Yaisel J. Borrell, Victor Gallego, Carmen García-Fernández, Ilaria Mazzeo, Luz Pérez, Juan F. Asturiano, Carlos E. Carleos, Emilia Vázquez, Jose A. Sánchez, Gloria Blanco

  3. Building genetic networks using relatedness information: a novel approach for the estimation of dispersal and characterization of group structure in social animals
    Molecular Ecology   DOI:10.1111/j.1365-294X.2012.05492.x
    Lee Ann Rollins, Lucy E Browning, Clare E Holleley, James L Savage, Andrew F Russell, Simon C Griffith

  4. Comparison of random and SSR‐enriched shotgun pyrosequencing for microsatellite discovery and single multiplex PCR optimization in Acacia harpophylla
    Molecular Ecology Resources 11 711-724   DOI:10.1111/j.1755-0998.2011.03002.x
    Olivier Lepais, Cecile F. E Bacles

  5. Cross-species amplification and development of microsatellites for six species of European Coenagrionid damselflies
    Conservation Genetics Resources   DOI:10.1007/s12686-011-9506-4
    Helena Johansson, Pär K. Ingvarsson, Frank Johansson

  6. Current trends in microsatellite genotyping
    Molecular Ecology Resources 11 591-611   DOI:10.1111/j.1755-0998.2011.03014.x
    E. Guichoux, L. Lagache, S. Wagner, P. Chaumeil, P. Léger, O. Lepais, C. Lepoittevin, T. Malausa, E. Revardel, F. Salin, R. J Petit

  7. De Novo Discovery and Multiplexed Amplification of Microsatellite Markers for Black Alder (Alnus glutinosa) and Related Species Using SSR-Enriched Shotgun Pyrosequencing
    Journal of Heredity   DOI:10.1093/jhered/esr062
    Olivier Lepais, Cecile Fanny Emilie Bacles

  8. Development and characterization of 24 polymorphic microsatellite loci in two Antirrhinum maju subspecies (Plantaginaceae) using pyrosequencing technology
    Conservation Genetics Resources   DOI:10.1007/s12686-011-9478-4
    Gabriel D. G. Debout, Emeline Lhuillier, Pierre-Jean G. Malé, Benoît Pujol, Christophe Thébaud

  9. Development of 18 microsatellite markers for the southern purple-spotted gudgeon (Mogurnda adspersa) from the lower Murray-Darling Basin through 454 pyrosequencing
    Conservation Genetics Resources   DOI:10.1007/s12686-011-9542-0
    Daniel C. Carvalho, Minami Sasaki, Michael P. Hammer, Luciano B. Beheregaray

  10. Development of 21 microsatellite markers for the threatened Yarra pygmy perch (Nannoperca obscura) through 454 shot-gun pyrosequencing
    Conservation Genetics Resources   DOI:10.1007/s12686-011-9413-8
    Daniel C. Carvalho, Clara J. Rodríguez-Zárate, Michael P. Hammer, Luciano B. Beheregaray

  11. Development of tetranucleotide microsatellite loci and a non-invasive DNA sampling method for Texas horned lizards (Phrynosoma cornutum)
    Conservation Genetics Resources   DOI:10.1007/s12686-011-9469-5
    Dean A. Williams, Cory Leach, Amanda M. Hale, Kristopher B. Karsten, Emmanuela Mujica, Diane Barber, Lee Ann Linam, Nathan Rains

  12. DNA sampling from eggshell swabbing is widely applicable in wild bird populations as demonstrated in 23 species
    Molecular Ecology Resources 11 481-493   DOI:10.1111/j.1755-0998.2010.02953.x
    David Martín‐Gálvez, Juan M Peralta‐Sánchez, Deborah A Dawson, Antonio M Martín‐Platero, Manuel Martínez‐Bueno, Terry Burke, Juan J Soler

  13. Isolation and characterization of microsatellite loci in Rhododendron ferrugineum (Ericaceae) using pyrosequencing technology
    American Journal of Botany 98 e120 -e122   DOI:10.3732/ajb.1000533
    Chloé E. L. Delmas, Emeline Lhuillier, André Pornon, Nathalie Escaravage

  14. Isolation and PCR-multiplex genotyping of 18 novel microsatellite markers for the threatened southern pygmy perch (Nannoperca australis)
    Conservation Genetics Resources   DOI:10.1007/s12686-011-9462-z
    Daniel C. Carvalho, Michael P. Hammer, Luciano B. Beheregaray

  15. Isolation of SSR markers for two African tropical tree species, Erythrophleum suaveolens and E. ivorense (Caesalpinioideae)
    American Journal of Botany   DOI:10.3732/ajb.1000482
    Jérôme Duminil, Guillaume K. Koffi, Gabriel Debout, Federico Sebastiani, Giovanni G. Vendramin, Myriam Heuertz, Santiago C. González-Martínez, Olivier J. Hardy

  16. Low level of extrapair parentage in wild zebra finches
    Animal Behaviour 79 261-264   DOI:16/j.anbehav.2009.11.031
    Simon C. Griffith, Clare E. Holleley, Mylene M. Mariette, Sarah R. Pryke, Nina Svedin

  17. Microsatellite resources for Passeridae species: a predicted microsatellite map of the house sparrow Passer domesticus
    Molecular Ecology Resources   DOI:10.1111/j.1755-0998.2012.03115.x
    Deborah A Dawson, Gavin J Horsburgh, Andrew P Krupa, Ian R. K Stewart, Sigrun Skjelseth, Henrik Jensen, Alexander D Ball, Lewis G Spurgin, Maria‐Elena Mannarelli, Shinichi Nakagawa, Julia Schroeder, Carl Vangestel, Gavin N Hinten, Terry Burke

  18. Molecular phylogeny reveals the existence of two sibling species in the aphid pest Brachycaudus helichrysi (Hemiptera: Aphididae)
    Zoologica Scripta   DOI:10.1111/j.1463-6409.2012.00531.x
    Joséphine Piffaretti, Flavie Vanlerberghe‐Masutti, Ashraf Tayeh, Anne‐Laure Clamens, Armelle Cœur D’acier, Emmanuelle Jousselin

  19. Multiplexed microsatellite markers for genetic studies of beech
    Molecular Ecology Resources   DOI:10.1111/j.1755-0998.2011.03094.x
    S. Lefèvre, S. Wagner, R. J Petit, G. De Lafontaine

  20. Rise of the machines – recommendations for ecologists when using next generation sequencing for microsatellite development
    Molecular Ecology Resources   DOI:10.1111/j.1755-0998.2011.03037.x
    Michael G Gardner, Alison J Fitch, Terry Bertozzi, Andrew J Lowe

  21. Targeted enrichment of genomic DNA regions for next-generation sequencing
    Briefings in Functional Genomics 10 374 -386   DOI:10.1093/bfgp/elr033
    Florian Mertes, Abdou Elsharawy, Sascha Sauer, Joop M.l.m. Van Helvoort, P.j. Van Der Zaag, Andre Franke, Mats Nilsson, Hans Lehrach, Anthony J. Brookes

  22. Thirteen microsatellites developed by SSR-enriched pyrosequencing for Solanum rostratum (Solanaceae) and related species
    American Journal of Botany 98 e296 -e299   DOI:10.3732/ajb.1100159
    Mario Vallejo-Marín, Lislie Solis-Montero, Cecile F. E. Bacles, Olivier Lepais

  23. Twenty-nine microsatellite markers for two Australian freshwater turtles, Elseya albagula and Emydura macquarii krefftii: development from 454-sequence data and utility in related taxa
    Conservation Genetics Resources 3 449-456   DOI:10.1007/s12686-010-9377-0
    Erica Todd, David Blair, Mark Hamann, Dean Jerry

  24. Two highly validated multiplexes (12‐plex and 8‐plex) for species delimitation and parentage analysis in oaks (Quercus spp.)
    Molecular Ecology Resources 11 578-585   DOI:10.1111/j.1755-0998.2011.02983.x
    E. Guichoux, L. Lagache, S. Wagner, P. Léger, R. J Petit