Bugfix release. Fixes serious issue affecting simulations with small sample sizes with mutations.

Bugfix release. Fixes serious issue affecting simulations with small
sample sizes with mutations.

https://github.com/jeromekelleher/msprime/issues/7

All users of mspms should update immediately and any analyses using
a small sample size (< 10) with mutations should be repeated.

Many thanks to Konrad Lohse for identifying the issue.

Bugfix release. Fixes serious issue affecting random seeds in mspms.

Bugfix release. Fixes serious issue affecting random seeds in mspms.

https://github.com/jeromekelleher/msprime/issues/6

All users of mspms should update immediately and any analyses using
the -seeds option in mspms should be repeated.

Many thanks to Derek Setter for identifying the issue.

Initial support for population structure in mspms

Transitional release providing population structure support for the
ms-compatible command line interface. A considerable amount of low-level
plumbing was required to provide the required flexibility. This is currently
not visible from the high-level API, but will shortly be made available in the
forthcoming 0.2.x series.

The current implementation of migration should work well for small numbers of
populations (e.g. < 10), but will not scale well for large numbers of
populations.

+++++++
Changes
+++++++

• Added the -I, -m, -ma, -em, -eM, -ema, -eG, -eg, -eN, -en,
  -ej and -es options to mspms. These should provide full ms
  compatability, except for the -es option which is currently
  limited in scope.
• Added some extra keys to the low-level configuration JSON in
  the HDF5 file format to describe the population structure.
  This will be documented in a future release.
• Added a get_pairwise_diversity method to the TreeSequence
  class to efficiently calculate the population genetics
  statistic pi.

Performance tweaks and bugfixes

Minor bugfix release:

• Performance improvements in simulation
• Changed default for max_memory parameter to unlimited
• Minor packaging changes.

Bugfix from 0.1.6a2

Fixes error in mspms's mutation position output.

Performance and bugfix release

• Updated simulation algorithm; ~20% faster for large simulations.
• Added proper SIGPIPE handling in msp
• Added precision argument for msp newick
• Fixed bug in mspms where the positions of mutations were incorrect.

Performance update

Fix version numbering error in previous alpha.

Performance update

This release tweaks the underlying simulation algorithm, and leads to ~20% performance improvements on large simulations.

Improved installation and performance

Changes from previous version:

• Installation instructions for Mac on Homebrew
• Improved documentations, removing TODO items.
• Added initial version of msp command line utility
• Added low-level LeafListIterator, improves performance of leaves() method.
• Improved performance of haplotype generation.

Minor bugfixes

Minor bugfix for CLI over 0.1.5a1.