The diameter (d) of the tool is a decisive factor for the calculation of cutting speed and rotational speed. Based on the available drive and its speeds, it is possible to calculate back which tool diameters can be used on the existing drive.

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Formatting input files for ∂a∂i (Gutenkunst 2009) and also some example scripts for demographic models, running ∂a∂i, obtaining summary statistics, reformatting output, etc.

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The drive speed (n) is specified in revolutions per minute [min-1]. The required speed is determined from the cutting speed V in meters per minute [m/min] or in meters per second [m/s] and the diameter of the tool d x π (3.14).

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Short read data from RAD-Seq of 8 individuals in each of 4 bird species (Rallus crepitans/obsoletus, Trochilus polytmus, Cranioleuca antisiensis, and Xenops minutus) (Harvey et al. 2015)

A program for simulating large sets of alignments resembling those obtained from massively parallel sequencing approaches like RAD-Seq and sequence capture of ultraconserved elements.

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Raw reads from sequence capture in 464 Amazonian birds used for comparative phylogeography of upland and floodplain habitats (Harvey et al. 2017, Am. Nat.)

Code plus phylogenies, sequence alignments, and other data used to examine diversification in suboscine passerines (Harvey et al. 2020).

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The cutting speed (v) is the speed at which a tool cutting edge is guided through the material to be machined in the cutting direction and removes a chip. The cutting speed V is specified in meters per minute [m/min] or in meters per second [m/s]. It depends on the speed of the drive n in revolutions per minute [min-1] and the diameter of the tool d x π (3.14).

We try to make all our data and software freely available and easily accessible. Scripts are generally available from Github, and data from NCBI, Dryad, or elsewhere. If you notice something that is missing, please contact us.

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Curated code and data used to compare population differentiation to speciation rates in New World birds (Harvey et al. 2017, PNAS)

A repository of miscellaneous Python code, mostly for processing and manipulating genetic data. Many of these are scripts for formatting input files for different phylogenetic and population genetics programs. Included are scripts for:

Formatting input files for BUCKy (Larget 2010) and running MrBayes (Huelsenbeck and Ronquist 2001) and mbsum iteratively on many loci

*Note that most of this code is not actively maintained, and it may depend on obsolete or deprecated releases or packages. It is provided as-is, generally under a 3-clause BSD license.