Data Resources

  • African-American/African-Caribbean recombination maps: Recombination maps infered from a sample of 2565 African Americans and 299 African Caribbeans.

  • Software

  • harp (Haplotype Analysis of Reads in Pools): Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data, developed by Darren Kessner (publication, download).

  • RASPberry (Recombination via Ancestry Switch Probabilities): Software for recombination rate inference machinery using ancestry switch points in admixed indivduals, developed by Daniel Wegmann.

  • simrecomb: Forward-in-time simulation of haplotype recombination, in multiple populations with admixture, developed by Darren Kessner.

  • MDBlocks: A program written with Eric Anderson that partitions a chromosomal segment into haplotype blocks using biallelic, phased haplotype data.

  • ENCprime: A program that calculates a codon usage bias summary statistic, Nc'. It is based on the effective number of codons statistic Nc (or ENC) developed by Frank Wright, but improves upon it by accounting for background nucleotide composition.

  • SIMCOAL: A program that uses a coalescent framework to simulate the evolution of multiple haploid populations with complex demographies . Developed by Laurent Excoffier and Stefan Schnieder with some contributions from myself. NOTE: A new version, SIMCOAL2, is now available SIMCOAL2.