Downloads
Protocols, Programs and Data sets from the Hamilton Lab
SpEED-Ne Matlab app to simulate and estimate genetic effective population size (N e ) from linkage disequilibrium
This Matlab app accompanies the paper:
Hamilton MB, Tartakovsky M, Battocletti A. 2018. SpEED‐Ne: Software to simulate and estimate genetic effective population size (Ne) from linkage disequilibrium observed in single samples. Molecular Ecology Resources 18(3):714-728.
https://doi.org/10.1111/1755-0998.12759
The app and code can be found on Github at github.com/mbhamilton/SpEED-Ne
This Matlab app accompanies the paper:
Hamilton MB, Tartakovsky M, Battocletti A. 2018. SpEED‐Ne: Software to simulate and estimate genetic effective population size (Ne) from linkage disequilibrium observed in single samples. Molecular Ecology Resources 18(3):714-728.
https://doi.org/10.1111/1755-0998.12759
The app and code can be found on Github at github.com/mbhamilton/SpEED-Ne
Microsatellite genotype data sets for striped bass and Matlab code to estimate RST.
These programs accompany the paper:
Brown KM, Baltazar GA and Hamilton MB. 2005. Reconciling nuclear microsatellite and mitochondiral marker estimates of populations structure: breeding population structure of Chesapeake Bay striped bass (Morone saxatilis). Heredity 94:606-615.
Data sets and Matlab programs (posted 13/06/2005).
Download striper.zip or striper.sit
The archives are less than 40K and contain a readme.txt file.
These programs accompany the paper:
Brown KM, Baltazar GA and Hamilton MB. 2005. Reconciling nuclear microsatellite and mitochondiral marker estimates of populations structure: breeding population structure of Chesapeake Bay striped bass (Morone saxatilis). Heredity 94:606-615.
Data sets and Matlab programs (posted 13/06/2005).
Download striper.zip or striper.sit
The archives are less than 40K and contain a readme.txt file.
|
| ||||
Microsatellite genotype data sets and Matlab code to estimate RST and bias in RST due to genotyping error.
These programs accompany the paper:
Adams, R. I, K. M. Brown and M. B. Hamilton. 2004. The impact of microsatellite electromorph size homoplasy on multilocus population structure estimates in a tropical tree (Corythophora alta) and an anadromous fish (Morone saxatilis). Molecular Ecology 13:2579-2588.
Data sets and Matlab programs (posted 10/01/2004).
Download homoplasy.zip or homoplasy.sit
The archives are less than 60K and contain a readme.txt file.
These programs accompany the paper:
Adams, R. I, K. M. Brown and M. B. Hamilton. 2004. The impact of microsatellite electromorph size homoplasy on multilocus population structure estimates in a tropical tree (Corythophora alta) and an anadromous fish (Morone saxatilis). Molecular Ecology 13:2579-2588.
Data sets and Matlab programs (posted 10/01/2004).
Download homoplasy.zip or homoplasy.sit
The archives are less than 60K and contain a readme.txt file.
|
| ||||
Chloroplast DNA Sequence Data and the T1Dand2D program to calculate Tajima's 1D and 2D
These programs accompany the paper:
Hamilton, M. B., J. M. Braverman, and D. Soria-Hernanz. 2003. Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in New World species of the Lecythidaceae. Molecular Biology and Evolution 20:1710-1721.
T1Dand2D (v. 6.4) program for MacOS, read me and example files (posted 09/08/2003).
Download T1Dand2D.sit (.sit archive that is about 128 K)
5 and 6 region chloroplast DNA sequence data files and substitution models
Download cpDNA_data.zip or cpDNA_data.sit
These programs accompany the paper:
Hamilton, M. B., J. M. Braverman, and D. Soria-Hernanz. 2003. Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in New World species of the Lecythidaceae. Molecular Biology and Evolution 20:1710-1721.
T1Dand2D (v. 6.4) program for MacOS, read me and example files (posted 09/08/2003).
Download T1Dand2D.sit (.sit archive that is about 128 K)
5 and 6 region chloroplast DNA sequence data files and substitution models
Download cpDNA_data.zip or cpDNA_data.sit
|
|
| ||||||
Matlab code for simulating nuclear and organelle population subdivision in an island model of gene flow
These programs accompany the paper:
Hamilton, M. B., and J. R. Miller. 2002 Comparing relative rates of pollen and seed gene flow in the island model using nuclear and organelle measures of population structure. Genetics 162:1897-1909.
Program to simulate nuclear and organelle population structure (posted 12/20/2002).
Download nucorg.zip or nucorg.sit
Program to estimate haploid subdivision with bootstrap confidence interval (posted 12/20/2002).
Download hapest.zip or hapest.sit
Archives are less than 25K and have readme.txt files.
These programs accompany the paper:
Hamilton, M. B., and J. R. Miller. 2002 Comparing relative rates of pollen and seed gene flow in the island model using nuclear and organelle measures of population structure. Genetics 162:1897-1909.
Program to simulate nuclear and organelle population structure (posted 12/20/2002).
Download nucorg.zip or nucorg.sit
Program to estimate haploid subdivision with bootstrap confidence interval (posted 12/20/2002).
Download hapest.zip or hapest.sit
Archives are less than 25K and have readme.txt files.
|
| ||||
|
| ||||
SNX Microsatellite Protocol
Download a detailed protocol to construct small-insert genomic libraries enriched for microsatellite repeat sequences (see Hamilton, M. B., E. L. Pincus, A. DiFiore, and R. Fleischer. 1999. Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. BioTechniques 27:500-507).
Download SNXmicro11.pdf (pdf file posted on 12/20/2002).
Older version:
Download SNXmicro.pdf (pdf file posted on 5/5/1999).
Download a detailed protocol to construct small-insert genomic libraries enriched for microsatellite repeat sequences (see Hamilton, M. B., E. L. Pincus, A. DiFiore, and R. Fleischer. 1999. Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. BioTechniques 27:500-507).
Download SNXmicro11.pdf (pdf file posted on 12/20/2002).
Older version:
Download SNXmicro.pdf (pdf file posted on 5/5/1999).
|
| ||||
