Software

Biology and Ecosystems

Learn more about animal population analysis, and access, explore, and download U.S. species occurrence data.

Filter Total Items: 70
Date published: April 14, 2020

CWD Simulation App

Chronic wasting disease (CWD) is a fatal disease of deer, elk, and moose transmitted through direct contact and via environmental contamination. This software provide tools to simulate CWD and harvest management scenarios. These models were developed by the U.S. Geological Survey (USGS) in collaboration with Montana Fish, Wildlife, and Parks.

Date published: March 16, 2020

Arctic Shorebird Population Model

This R script will run one example of the stochastic matrix models run by Weiser et al. (in review) to simulate shorebird populations. The model predicts population growth rates and elasticity values of vital rates. The example script is stand-alone and contains input values for one example species; input values for the other species are provided in the manuscript.

Date published: October 19, 2018

GenEst - A Generalized Estimator of Mortality

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

Date published: 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.

Date published: August 13, 2018

bi-transect-extractor

This package is used to calculate coastal geomorphology variables along shore-normal transects. The calculated variables are used as inputs for modeling geomorphology using a Bayesian Network (BN). 

Date published: August 6, 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.

Date published: July 3, 2018

Bandit Software

Bandit is the latest in a series of desktop applications aimed at helping bird banders manage and submit their data for banded birds. We have tried to make the process of maintaining banding records as simple as possible. Bandit was created by the Bird Banding Laboratory (BBL) at the USGS Patuxent Wildlife Research Center, Laurel, MD.

Date published: June 25, 2018

iPlover

iPlover was developed by the U.S. Geological Survey Woods Hole Coastal and Marine Science Center and the USGS Center for Integrated Data Analytics.  It is used by trained and vetted personnel to record information about habitats on coastal beaches and he environment surrounding them. 

Date published: April 23, 2018

Ecosheds.org

LSC Conte Anadrmous Fish Laboratory is currently involved in https://ecosheds.org.

Date published: January 26, 2018

Composite Raster and Divergence Tool

The Composite Raster and Divergence Tool is an ArcGIS ArcMap add-in

Date published: January 25, 2018

SPARROW modeling: Estimating contaminant transport

 

What’s New: A new version of the SPARROW code is being developed in the R programming language. The advantage of R is that it is non-proprietary and does not require a license or software cost. The R – SPARROW code is now being completed and should be available early in CY18. Stay Tuned.

Date published: November 14, 2017

fatalityCMR

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