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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| readme.mkd | 2012-12-14 | 1.2 kB | |
| popbam-0.2.tar.gz | 2012-12-14 | 111.7 kB | |
| Totals: 2 Items | 112.9 kB | 0 | |
The beta version 0.2 of POPBAM has finally been released!
New functionality includes:
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Three new measures of linkage disequilibrium: omega_max (Kim and Nielsen 2004), ZnS Kelly(1997) and Wall's Q (Wall 1999).
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Haplotype-based statistics such as number of haplotypes, minimum interpopulation haplotype distance, and the site-specific extended haplotype homozygosity statistic of Tang (2007).
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The new diverge function which can be used to calculate divergence with reference sequence (or a specified outgroup sequence) to calculate substitution rates.
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The snp function has the ability to write raw polymorphism data to ms and SweepFinder formatted output.
Other changes and improvements to the software include:
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The fasta function has been deprecated.
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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.