Working notes for 2013

Using AlloppNET for diploids and allotetraploids

2013-05-06. Draft article as PDF. Draft article as Latex. Figures for draft article.

2013-05-14. Manual and examples. ZIP file containing PDF manual, R scripts (Silene2-makebeastxml.r + parts of 'AlloppDT') and example data (4 nex files plus taxa table).

AlloppNET code

2013-10-26. R scripts used to run simulations for AlloppNET for diploids and allotetraploids.

Dissect

2013-10-06. Multilocus species delimitation model ('Dissect') in BEAST. Draft 2 of supplementary information

2013-08-29. Example BEAST XML for Dissect.

2013-10-08. Draft Application note (for Bioinformatics): Multilocus species delimitation in BEAST

Dissect code

2013-10-26. R scripts used to run simulations for Dissect.

PopsIO

2013-09-24. Simple population model A multispecies coalescent model with the population parameters integrated out. This descibes the calculations to be done by the software