Daniel Garrigan

The beta version 0.2 of POPBAM has finally been released!

New functionality includes:

  • Three new measures of linkage disequilibrium: omega_max (Kim and Nielsen 2004), ZnS Kelly(1997) and Wall's Q (Wall 1999).

  • Haplotype-based statistics such as number of haplotypes, minimum interpopulation haplotype distance, and the site-specific extended haplotype homozygosity statistic of Tang (2007).

  • The new diverge function which can be used to calculate divergence with reference sequence (or a specified outgroup sequence) to calculate substitution rates.

  • The snp function has the ability to write raw polymorphism data to ms and SweepFinder formatted output. The snp function also now has an option to call heterozygous sites.

Other changes and improvements to the software include:

  • Removal of the dependency on the libbam library, successful build of popbam now only requires zlib to link properly.

  • The fasta function has been deprecated.

  • Version 0.2 includes an updated base-calling model that accounts for correlations in errors on the same strand during amplification.

  • The second beta release includes numerous bug fixes, most importantly, in the tree and sfs functions.

In the future, the ability to read features from a GFF file is planned for release candidate 1.0.

If you would like to suggest additional functionality or become a beta-tester, please contact Dan Garrigan at dgarriga@bio.rochester.edu.