fasta2nexus

fasta2nexus (deprecated): Function for converting molecular alignments from fasta to nexus format

Functions are provided for prior specification in divergence time
estimation using fossils as well as other kinds of data. It
provides tools for interacting with the input and output of Bayesian
platforms in evolutionary biology such as 'BEAST2', 'MrBayes', 'RevBayes',
or 'MCMCTree'.
It Implements a simple measure similarity between probability
density functions for comparing prior and
posterior Bayesian densities, as well as code for calculating the
combination of distributions using conflation of Hill (2008). Functions for estimating the
origination time in collections of distributions using the x-intercept (e.g., Draper and Smith, 1998) and
stratigraphic intervals (Marshall 2010) are also available.
Hill, T. 2008. "Conflations of probability distributions". Transactions of the American Mathematical Society, 363:3351-3372. <doi:10.48550/arXiv.0808.1808>,
Draper, N. R. and Smith, H. 1998. "Applied Regression Analysis". 1--706. Wiley Interscience, New York. <DOI:10.1002/9781118625590>,
Marshall, C. R. 2010. "Using confidence intervals to quantify the uncertainty in the end-points of stratigraphic ranges". Quantitative Methods in Paleobiology, 291--316. <DOI:10.1017/S1089332600001911>.

Gustavo A. Ballen

tbea

Pre- And Post-Processing in Bayesian Evolutionary Analyses

Sandra Reinales

fasta2nexus function

<dl><dt>...</dt>
<dd>A placeholder for any argument that used to be in this function.</dd></dl>

Arguments

Author

fasta2nexus (deprecated): Function for converting molecular alignments from fasta to nexus format — fasta2nexus

<dl>

<dt>...</dt>
<dd>A placeholder for any argument that used to be in this function.</dd>

</dl>

fasta2nexus: fasta2nexus (deprecated): Function for converting molecular alignments from fasta to nexus format

Description

Usage

Value

Arguments

Author

Details