Which version is the most up to date?

[Matthew Olson]

We are loading dppdiv onto a new computer and are a bit confused about which version to use. We noticed that there is an update at https://github.com/trayc7/FDPPDIV, but there was a previous update by a different user at https://github.com/ddarriba/pll-dppdiv. Also, there is a parallelized version at http://sco.h-its.org/exelixis/software.html. 

Could you provide some guidance about which version is the most up-to-date regarding both bug fixes and efficiency of computation? Are there additional versions that we should be aware of?

thanks

[Tracy Heath]

Hi Matt,

This is a good question. The versions that Diego Darriba, Tomas Flouri, and Alexis Stamatakis are working on include their Phylogenetic Likelihood Library (PLL) described in this paper: http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2013-2.pdf. I forked a version of their development code that just includes the optimized likelihood functions for SSE, AVX, and OpenMP. And that's what's in https://github.com/trayc7/FDPPDIV. So the version that includes the PLL is definitely faster. And I believe they have also implemented amino acid models. However, my development version has some new models for fossil calibration. At the moment, I recommend working with their versions since the fossil-calibration models have only been tested on a subset of realistic datasets. Ultimately, the new models I'm working on will be merged with their code. 

Cheers!

Tracy

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