BiK-F  

Software Downloads

siMBa
BiK-F-researcher Bagdevi Mishra from Marco Thines' lab has developed siMBa - a simple graphical user interface for the Bayesian phylogenetic inference program MrBayes, which gives the user interactive control over most of the parameters and also facilitates the input of a multiple sequence alignment, as any widely used format can be used.
siMBa is available for download under http://thines-lab.senckenberg.de/simba
An article with more details is available here:
http://download.springer.com/static/pdf/23/art%253A10.1007%252Fs11557-014-1010-2.pdf?auth66=1410987579_63b09585bf34d6541df39ffbb59cf440&ext=.pdf

Bayesian approach to estimate rates of species diversification
BiK-F researchers Daniele Silvestro and Jan Schnitzler have developed a novel Bayesian approach to estimate rates of species diversification from molecular phylogenies. The method is highly flexible and allows testing hypotheses on differential diversification rates through time or between geographic regions under a range of models while accounting for incomplete taxon sampling and phylogenetic uncertainty.
The method has recently been published in the journal BMC Evolutionary Biology and is implemented in the program "BayesRate", which is available for free at: http://sourceforge.net/projects/bayesrate/
If you have any questions, please contact Daniele Silvestro (dsilvestro[at]senckenberg.de) or Jan Schnitzler (jan.schnitzler[at]senckenberg.de).
Silvestro, D.*, Schnitzler, J.* & G. Zizka (2011): A Bayesian framework to estimate diversification rates and their variation through time and space. - BMC Evolutionary Biology 11:311. (* equal contribution)

 raxmlGUI
The BiK-F members Daniele Silvestro and Ingo Michalak have developed the add-on "raxmlGUI"  for the program "RAxML" (Stamatakis 2006). The tool considerably simplifies the use of phylogenetic analyses with RAxML.
Here, you can download it for free (with incorporated RAxML).
If you have any questions, please contact Daniele Silvestro or Ingo Michalak.
Silvestro, D. and Michalak, I. (2011) raxmlGUI: a graphical front-end for RAxML. Organisms Diversity & Evolution. DOI: 10.1007/s13127-011-0056-0
Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690.