I just announce that the tr2-delimitation in Python3 is now available from the following repository.
It should return results exactly the same as the Python2 version (I verified it with the data set of the Fujisawa et al. (2016) paper).
I will maintain the old Python2 version, but the new functions will be added to this Python3 version.
I just announce that the codes for the new multilocus delimitation method are available at my Bitbucket repository.
The new program is called “tr2”, which stands for “trinomial distribution of triplets” model. It delimits species from multilocus gene trees by measuring congruence of gene trees between species and incongruence within species. It calculates the posterior probabilities of two types of trinomial distribution models and test within/between-species boundaries. A closely related methods are MP-EST, the triplet-based phylogeny reconstruction method by Liu et al, and the Bayesian species delimitation method BP&P by Yang&Rannala.
The tr2 implements a rapid algorithm to find the best delimitation under a given guide tree and an optimality score (AIC or posterior probability), which can run with more than 100 tip guide trees.
If you are interested in it, please visit the repository below and try it.
I assume that users have knowledge of Python and related programming tools like Mercurial. The program is not well-decumented now. I will write down detailed instructions in following blog posts.
Some new papers on DNA based species delimitation have been published.
A paper about a mutilocus species delimitation method has just been published.
Fujisawa, T., Aswad, A. and Barraclough, T.G. (2016) A rapid and scalable method for multilocus species delimitation using Bayesian model comparison and rooted triplets. Syst.Biol. doi: 10.1093/sysbio/syw028
It describes a new multilocus species delimitation method which is applicable to large data.
Another paper I coauthored is about the GMYC and taxon sampling.
Ahrens, D. Fujisawa, T., Krammer, HJ., Eberle, J., Fabrizi, S. and Vogler, A.P. (2016) Rarity and Incomplete Sampling in DNA-based Species Delimitation. Syst. Biol. doi:10.1093/sysbio/syw002
It is about empirical and simulation studies about the effects of different taxon sampling schemes on the single locus delimitation method.
A new paper about molecular evolution of water beetles is now published.
Fujisawa, T., Vogler, A.P., Barraclough T.G. (2015) Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles. Proc. R. Soc. B. 282:20142476
It is about ecological correlates on species’ genetic variation and rate of molecular evolution. Also, it is an application of the GMYC delimitation to comparative analysis based on sequence databases.
The problem was solved. Now, the splits is available for download from the R-forge.
The R-forge site for the splits is now experiencing a problem of package building. Both source files and the binary package are not available for download. The install.packages command described in “how to install” do not work either. It is unclear when this problem is solved.
I put the source code and package file on Github for now.
This is only for temporary download. I have not decided whether the package will be hosted on Github or not.
If you are not familiar with how to use Git, a simple way to install package is following:
0) Make sure you installed the latest R and dependency packages.
1) Click the “Download ZIP” button at the bottom right to download the zipped files.
2) Decompress “splits_1.0-19.tar.gz” from the downloaded zip file.
3) Call install.pacakges on your R console to install from the local file.
A server version of the GMYC is now available thanks to Jiajie Zhang at Heidelberg Institute for Theoretical Studies.
This server also implements another single locus delimitation method called PTP, which works on non-ultrametric trees.
If you do not really like running commands on your R console, please try the server version.
Two papers I was working on have been finally published.
Fujisawa, T. and Barraclough T.G. (2013) Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent (GMYC) approach: A revised method and evaluation on simulated data sets. Syst.Biol. doi:10.1093/sysbio/syt033
Baselga, A., Fujisawa, T., Crampton-Plat, A., Bergsten, J., Foster, P.G., Monaghan, M.T. and Vogler, A.P. (2013) Whole-community DNA barcoding reveals a spatiotemporal continuum of biodiversity at species and genetic levels. Nat. Commun. 4:1892
The first paper is about the GMYC, and the second is a more ecology-oriented paper trying to characterize genetic and species compositions of communities.
Now the GMYC paper is open-access thanks to the support of college.