Installation

tapir has several dependencies. At a minimum you will need to install:

Installing hyphy

tapir uses hyphy for substitution model selection and site rate estimation. Additionally, hyphy needs to be compiled as a single-threaded binary. We provide appropriate binaries for:

You need to download these and place them within your $PATH. If this statement confuses you, then you should read this article on UNIX paths.

Installing numpy

You first need to install numpy. Barring platform-specific options, you can accomplish this by running:

easy_install numpy

Sometimes on OSX, this is problematic. There is a numpy binary installer that you can use in this case.

Installing scipy

You also need to install scipy. Barring platform-specific options, you can accomplish this by running:

easy_install scipy

Sometimes on OSX, this is problematic. There is a scipy binary installer that you can use in this case.

Installing dendropy

Installing dendropy is easy using easy_install:

easy_install dendropy

rpy2 [optional]

To produce pretty and relatively pain-free graphics, you will need to install rpy2. This is generally easily done using:

easy_install rpy2

Although this is currently not working on OSX Lion (see here for temporary workaround).

matplotlib [optional]

To produce more basic figures, you can use matplotlib which is installed using:

easy_install matplotlib

tapir computes the phylo-genetic informativeness of DNA loci

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