Software

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September 26, 2019

popcluster: Developing Hierarchical Population Monitoring Frameworks for mobile species with high site fidelity

The software "popcluster" constructs hierarchically nested groupings of similar habitats associated with field surveys while considering biological structure/connectedness (movements between habitats). This approach can support mobile species with high site fidelity where monitoring during surveys occurs on birthing grounds, breeding grounds, or stopovers/seasonal habitat for migratory species. Ea

Ecosystems Mission Area, Land Management Research Program, Fort Collins Science Center

December 18, 2018

Python Scripts for Bioinformatics, 2017

Bioinformatics software repository containing python scripts intended for search and download of genetic information obtained from GenBank NCBI genetics data resources in support of developing PCR primers, targeted genetic databases, genetic analyses, and data interpretation. Includes multiple functions to streamline this process. This repository represents an effort to strengthen the software c

Ecosystems Mission Area, Species Management Research Program, Alaska Science Center, Molecular Ecology Laboratory

October 19, 2018

GenEst - A Generalized Estimator of Mortality

GenEst, a generalized estimator of wildlife mortality at renewable energy facilities.

Ecosystems Mission Area, Forest and Rangeland Ecosystem Science Center

September 27, 2018

Sea lamprey quantitative environmental DNA surveillance

The data set is six separate csv files. Four of which contain the quantity of DNA copy numbers and fluor used to analyze the DNA quantities collected from water samples from four separate portions of the study (adult SL field, adult SL lab, larval SL field, larval SL lab) and need to be in their own csv file. Also included is a csv with adult SL trapping data, a csv for larval SL shocking data, a

Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Upper Midwest Environmental Sciences Center

August 21, 2018

SSR_pipeline: Computer Software for the Identification of Microsatellite Sequences from Paired-End Illumina High-Throughput DNA Sequence Data

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (SSRs; for example, microsatellites) from paired-end high-throughput Illumina DNA sequencing data.

Ecosystems Mission Area, Forest and Rangeland Ecosystem Science Center

February 12, 2018

Data Retrieval and Graphing Using the LTRM Fish Catch GeoJSON Data Service

UMESC hosts a web service for the retrieval of LTRM fish catch data using the GeoJSON data format. By using this data service, the public can automate data access to LTRM fisheries data. UMESC has written a series of example Python scripts that illustrate data retrieval and plotting. These example scripts focus on plotting fish catch, but there are limitless geo-spatial, tabular, and plotting pr

Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Upper Midwest Environmental Sciences Center

November 14, 2017

fatalityCMR

Capture-recapture software to correct raw counts of wildlife fatalities using trial experiments for carcass detecition probability and persistence time.

Ecosystems Mission Area, Eastern Ecological Science Center

July 6, 2017

Evidence of Absence (EoA) Software and User's Guide

Software to Estimate Bird and Bat Fatality at Wind Farms

Ecosystems Mission Area, Forest and Rangeland Ecosystem Science Center

March 9, 2017

AquaPathogen X: A Template Database for Tracking Field Isolates of Aquatic Pathogens

Aquatic Pathogen Template Database (AquaPathogen X)

Ecosystems Mission Area, Western Fisheries Research Center, Fish Health Program (FHP)

March 8, 2017

Random Landscape Tool 10.5

Random Landscape Tool uses a raster data source and a table of classifications to create a random landscape. The classification table allows the user to weight the probability of occurrence to certain classes and to spatially restrict the distribution of classes to certain areas (zones).

Ecosystems Mission Area, Land Management Research Program, Upper Midwest Environmental Sciences Center

December 11, 2012