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Research organizations, government departments, and companies

  • U.S. Fish and Wildlife Service (USA)
  • National Marine Fisheries Service (USA)
  • National Istitute of Water and Atmospheric Research (New Zealand)
  • CSIRO (Australia)
  • Cefas (UK)
  • Fisheries and Oceans Canada (Canada)
  • Danish Institute for Fisheries Research (Denmark)
  • L’Institut de recherche pour le développement (IRD) (France)
  • Inter-American tropical Tuna Commission(International)
  • International Pacific halibut Commission (International)
  • Secretariat of the Pacific Community (International)
  • Commission for the Conservation of Southern Bluefin Tuna (International)
  • International Whaling Commission (International)
  • Great Lakes Indian Fish and Wildlife Commission (USA Inter-tribal)
  • Modeling subcommittee, Technical Fisheries Committee, 1836 Treaty Waters, Michigan, USA (Chippewa Ottawa Resource Authority and associated tribes, Michigan Department of Natural Resources (Charlevoix, Alpena and Marquette Fisheries Stations), USFWS (Green Bay, Alpena, Ashland)).
  • Columbia River Inter-Tribal Fish Commission (USA Inter-tribal)
  • Minnesota Department of Natural Resources (USA)
  • International Commission for the Conservation of Atlantic Tunas (not sure if this is the commission or the individual countries)
  • Indian Ocean Tuna Commission (not sure if this is the commission or the individual countries)
  • National Research Institute of Far Seas Fisheries (NRIFSF) (Japan)
  • Quantitative Resource Assessment LLC (USA)
  • Marine Research Centre, Malé, (Republic of Maldives)
  • Institute of Marine Research, Nordnes, (Norway)
  • Marine and Coastal Management, Cape Town, (South Africa)
  • Seafood Industry Council (SeaFIC), Wellington, (New Zealand)
  • Trophia, (New Zealand)
  • British Antarctic Survey, Cambridge, (UK)
  • International Commission for the Conservation of Atlantic Tunas
  • Department of Fisheries Western Australia
  • Okeanos-Oceanides Consortium for Conservation and Marine Development (Mexico)
  • Fairport Fisheries Research Station, ODNR, Division of Wildlife (USA)
  • Centro Nacional Patagonico (Argentina)
  • Instituto Nacional de Investigacion y Desarrollo Pesquero (Argentina)


  • University of Washington (USA - Andre Punt)
  • Quantitative Fisheries Center, Michigan State University (USA - Jim Bence, Michael Jones co-directors, Travis Brenden associate director)
  • Tokyo University of Agriculture (Japan - Minoru Kanaiwa - Multispecies statHBS)
  • University of Auckland (New Zealand - Russell Millar)
  • Cornell University (USA - Patrick Sullivan)
  • University of British Columbia (Canada - Steve Martell)
  • University of Cape Town (South Africa - Doug Butterworth)
  • Universidad de Concepción (Chile - Billy Ernst)
  • University of Rhode Island (USA - Jeremy Collie)
  • Simon Fraser (Canada - Sean Cox)
  • University of Bergen (Norway - Hans Julius Skaug)
  • University of Tasmania (Australia - Malcolm Haddon)
  • Murdoch University (Australia - Norm Hall)
  • National Taiwan University (Taiwan - Chi-Lu Sun/Sheng-Ping Wang)
  • University of Maine, Orono (USA - Yong Chen)
  • University of Hawaii, Honolulu (USA - John Sibert - Anders Nielsen)
  • University of Oslo (Norway - Dinara Sadykova)
  • Tokyo University of Marine Science and Technology (Japan - Toshihide Kitakado)
  • Universidade Estadual de Maringá (Brasil - Carolina V. Minte-Vera)

Major Applications

MULTIFAN-CL: MULTIFAN-CL is a computer program that implements a statistical, length-based, age-structured and spatial-structured model for use in fisheries stock assessment. The model is a convergence of two previous approaches. The original MULTIFAN model (Fournier et al. 1990) provided a method of analysing time series of length-frequency data using statistical theory to provide estimates of von Bertalanffy growth parameters and the proportions-at-age in the length-frequency data. The model and associated software were developed as an analytical tool for fisheries in which large-scale age sampling of catches was infeasible or not cost effective, but where length-frequency sampling data were available. MULTIFAN provided a statistically-based, robust method of length-frequency analysis that was an alternative to several ad hoc methods being promoted in the 1980s. The Western Central Pacific Fish Commission for the Conservation and Management of Highly Migratory Fish Stocks in the Western and Central Pacific Ocean (WCPFC) depends on MULTIFAN-CL for assessment of skipjack, yellowfin, bigeye and albacore tuna stocks. MULTIFAN-CL has also been used for assessment of blue sharks, swordfish, and blue marlin in the Pacific.

Stock Synthesis NOAA Fisheries Toolbox Version Version 3.24f (October 2012). Stock Synthesis of SS provides a statistical framework for calibrating a population dynamics model with a diversity of fishery and survey data. The program can accommodate both age and size structure, with multiple stock sub-areas.

trackit and kftrack/kfsst: state-space models for reconstructing tracks produced by electronic tags. This software can be applied directly to solar irradiance time series recorded by archival tags or to position estimates produced by other algorithms. These programs have have become the methods of choice in many laboratories.

SEAPODYM is model for investigating physical-biological interaction between tuna populations and the oceanic ecosystem. Using predicted environment from ocean-biogeochemical models, SEAPODYM integrates spatio-temporal and multi-population dynamics and considers interactions among populations of different species and between populations and their physical and biological environment (including intermediate trophic levels). The model also includes a description of multiple fisheries and then predicts spatio-temporal distribution of catch catch rates, and length-frequencies of catch based either on observed or simulated fishing effort. Applications of SEAPODYM include management strategy evaluation, predicting effects of global warming, design of time-area closures. SEAPODYM-APE is a Adjoint Parameter Estimation procudure build on the AUTODIF library that estimates tuna population dynamics parameters from fisheries data.

A-SCALA: Age-Structured Statistical Catch-at-Length Analysis used at the Inter-American Tropical Tuna Commission for assessment of tuna stocks in the Eastern Pacific Ocean. A-SCALA is based on the MULTIFAN-CL modeling framework. A-SCALA has been used to assess tuna stocks in the eastern Pacific Ocean for the past 8 years. The species assessed include yellowfin, skipjack, and bigeye tuna. A-SCALA has also been applied to bigeye tuna in the western and central Pacific Ocean.

Coleraine: A generalized age structured stock assessment model. Coleraine has been used in several countries to assess the status of many fish stocks (e.g. US: sablefish, short spine thornyhead, ling, Pacific herring, various rockfish; Canada: albacore tuna, rock sole; New Zealand: southern blue whiting, orange roughy, smooth oreo, rig; Australia: silver trevally, jackass morwong, pink ling, redfish; Chile: lobster, shrimp; Iceland: cod). Coleraine was used to provide examples and was included as a tool in the Food and Agriculture Organization of the United Nations’ Bayesian stock assessment user’s manual. Coleraine has been used in several university courses (e.g. the courses “Age Structured Modeling” FISH 507 and “Advanced Fisheries Stock Assessment” FISH 558 at the University of Washington. The course “Evaluacion de Stock” at the Universidad de Concepcion, Chile).

statHBS: A statistical version of the habitat based method to standardize catch and effort data from longline fisheries. This is a nonlinear model that has had applications that have included data sets with hundreds of thousands of data points. This model has been used by the Secretariat of the Pacific Community, the US National Marine Fisheries Service, the National Research Institute for far Seas Fisheries, Japan, Australian Commonwealth Scientific and Industrial Research Organisation, and the International Scientific Committee for Tuna and Tuna-like Species in the North Pacific Ocean. The model has been applied to several Pacific HMS species including: bigeye and yellowfin tuna, striped marlin and blue shark. Funding has been acquired by the US National Marine Fisheries Service from the Pelagic Fisheries Research Program to develop it further.

A generalized assessment and management strategy evaluation model for marine mammals: This model was funded by the New Zealand Department of Conservation and was applied to the New Zealand sea lion population. Its has also been adapted to other marine mammal stocks in New Zealand (e.g. Hectors and Maui dolphin)

Case specific models for Alaska groundfish
These age-structured models were developed from a core set of routines at the Alaska Fisheries Science Center. They include assessment applications to three different stocks of Alaska pollock, Alaska-wide sablefish, eight stocks of flatfish, seven stocks of rockfish, and Atka mackerel in the Bering Sea and Aleutian Islands. Overall, these assessments are used to manage nearly two million tons of catch each year.

A Bayesian seasonal and sex-specific length-structured assessment model for the American lobster stocks: This model is developed for assessing the American lobster fishery in the northeastern United States. It is funded by the Maine Sea Grant College Program, Maine Department of Marine Resources, and Atlantic States Marine Fisheries Commission.

Stocks for which recent assessments rely on ADMB, AutoDiff or their derivatives. (add annual value of fishery in $US after each stock/species if known)

University of cape Town - South Africa


  • African penguin
  • Sardine
  • Anchovy
  • Rock lobster

Quantitative Fisheries Center, Michigan State University


  • Yellow perch - Lake Michigan
  • Chinook salmon - Lakes Michigan and Huron
  • Sea lamprey - St. Marys River, Lake Huron

Modeling subcommittee, Technical Fisheries Committee, 1836 Treaty Waters


  • Lake whitefish - Lakes Michigan, Huron, and Superior
  • Lake trout - Lakes Michigan, Huron, and Superior

California Department of Fish and Game

Stock Synthesis

  • California Scorpionfish

IATTC (US$ 1.5 Billion)

Stock Synthesis

  • Swordfish
  • Bigeye Tuna


  • Yellowfin Tuna
  • Skipjack Tuna
  • stripped marlin
  • Hawaiian Black footed albatross
  • Spotted dolphin



  • Yellowfin Tuna
  • Albacore Tuna
  • Bigeye Tuna
  • Skipjack tuna


Stock Synthesis

  • Northern bluefin tuna (Japan Far Seas Lab/NMFS)
  • Albacore (NMFS)
  • Swordfish (NMFS)


Stock Synthesis

  • Jackass Morwong
  • Silver Trevally
  • Tiger Flathead
  • Eastern Gemfish
  • School Whiting
  • Blue Warehou
  • Pink Ling
  • Spotted Warehou
  • Eastern Zone Orange Roughy
  • Cascade Orange Roughy
  • Elephant fish
  • Bight Redfish
  • Deepwater Flathead


  • Blue grenadier
  • Redfish
  • Saw shark
  • Gummy Shark
  • Macquarie Island toothfish
  • Tiger and endeavour prawn assessment, Northern Prawn Fishery

University of Tasmania


  • Tasmanian Rock Lobster


Stock Synthesis

  • BSAI Greenland turbot
  • BSAI Pacific cod
  • GOA Pacific cod
  • North Pacific albacore tuna
  • Pacific coast Blackgill rockfish
  • Pacific coast Cabezon
  • Pacific coast Canary rockfish
  • Pacific coast Chilipepper rockfish
  • Pacific coast Cowcod
  • Pacific coast Dark-blotched rockfish
  • Pacific coast Dover sole
  • Pacific coast English sole
  • Pacific coast Gopher rockfish
  • Pacific coast Lingcod
  • Pacific coast longnose skate
  • Pacific coast Longspine thornyhead
  • Pacific coast Pacific Ocean perch
  • Pacific coast Pacific sardine
  • Pacific coast Pacific whiting
  • Pacific coast Petrale sole
  • Pacific coast Sablefish
  • Pacific coast Shortspine thornyhead
  • Pacific coast Starry flounder
  • Pacific coast Yelloweye rockfish
  • Pacific coast Yellowtail rockfish
  • Pacific coast Baccacio


  • Pacific blue shark
  • North Pacific swordfish
  • North Pacific bluefin tuna


  • Aleutian Islands Atka mackerel
  • Aleutian Islands pollock
  • Bogoslof pollock
  • Alaska-wide projection model
  • Pacific coast Widow rockfish SCA
  • BSAI Northern rockfish
  • BSAI Pacific ocean perch
  • BSAI Alaska plaice
  • BSAI flathead sole
  • BSAI northern rock sole
  • BSAI Arrowtooth Flounder
  • BSAI Shortraker/Rougheye
  • BSAI Snow crab
  • BSAI yellowfin sole
  • EBS Pollock
  • GOA Arrowtooth Flounder
  • GOA Dover sole
  • GOA Northern rockfish
  • GOA Pacific ocean perch
  • GOA pollock
  • GOA Rex sole
  • GOA Rougheye rockfish
  • GOA Shortraker rockfish
  • Alaska Sablefish
  • Acadian redfish
  • Atlantic herring
  • Atlantic mackerel
  • Georges Bank cod
  • Gulf of Maine cod
  • Gulf of Maine winter flounder
  • NE Ocean quahog
  • NE Sea scallops
  • Southern New England winter flounder
  • NE Surf clam
  • Atlantic menhaden
  • SE black sea bass
  • SE cobia
  • SE gag grouper
  • SE Goliath grouper
  • Gulf of Mexico greater amberjack
  • SE greater amberjack
  • SE grey triggerfish
  • Gulf menhaden
  • SE Lane snapper
  • SE large coastal sharks
  • SE red grouper
  • SE red porgy
  • Gulf of Mexico red snapper
  • SE small coastal sharks
  • SE snowy grouper
  • SE tilefish
  • SE vermilion snapper SCL-VRS
  • Gulf of Mexico vermilion snapper
  • SE yellowedge grouper
  • SE Sandbar shark
  • Longfin squid
  • Atlantic white marlin



  • Yellow-eye penguin
  • New Zealand Sea Lion
  • Hector’s Dolphin - Model estimates for Banks Peninsula subpopulation; risk analysis for three subpopulations around the South Island, New Zealand.
  • Maui’s Dolphin - risk analysis using Bayesian estimates from Banks Peninsula model.
  • CRA3 and NSS, NSN substock and the combined CRA 4 and CRA 5 stock of red rock lobster (Jasus edwardsii)
  • paua (Haliotis iris) in PAU 7, PAU 5B and PAU 5D
  • cockles on Snake Bank


Stock Synthesis

  • Bigeye tuna (Japan far seas)

Undersecretary of Fisheries, Ministery of Economy, Chile


  • skate (Raja flavirostris)
  • south Pacific swordfish (Xiphias gladius)

DFO Canada


  • Hecate St rocksole


  • Sablefish
  • Hecate Strait Pacific cod
  • Pacific Ocean perch assessment for the West Coast of Canada
  • Porbeagle Shark (Lamna nasus) Population in the Northwest Atlantic
  • anadromous alosa
  • Hecate St English sole
  • Queen Charlotte Sound English sole
  • West Coast BC Petrale sole

Commission for the Conservation of Southern Bluefin


  • Bluefin tuna

International Pacific Halibut Commission


Pacific Halibut

Great Lakes Indian Fish and Wildlife Commission


  • Walleye, northern pike, and yellow perch in Mille Lacs Lake
  • Walleye in inland Wisconsin Lakes
  • Lake trout in Lake Superior

Minnesota Department of Natural Resources


  • Walleye in Mille Lacs Lake



  • Branch, T.A. & Butterworth, D.S. 2006a. Assessment of the East Greenland-Iceland fin whale



  • Orange Roughy
  • SPO7 rig



  • TRE7 Trevally
  • Yellow-eye penguin (see NIWA/MFish)

Quantitative Resource Assessment LLC

Stock Synthesis

  • California scorpionfish (see California Department of Fish and Game)

British Antarctic Survey - Cambridge, UK


  • Antarctic penguins
  • Adelie, chinstrap and gentoo penguin population dynamics at South Georgia and South Orkney Islands

International Commission for the Conservation of Atlantic Tunas


  • Atlantic Bigeye Tuna
  • N. Atlantic Albacore

Department of Fisheries Western Australia


  • Western Rock Lobster

University of Maine (Orono)


  • Maine green sea urchin fishery ($10 million)
  • American lobster fishery in the northeastern USA (Gulf of Maine stock, Georges Bank stock, and Southern New England stock)($1 billion)

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