markophylo specifications


Unique identifier OMICS_09936
Name markophylo
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A phylogenetic tree with branch lengths in units of expected substitutions per site and a matrix containing phyletic patterns of discrete characters are the primary external inputs needed for markophylo. The tree must be in the phylo format of the APE package, while each row of the matrix represents a phyletic pattern, where the columns denote closely related taxa of interest.
Output data The output from the primary function contains parameter estimates for the user-specified substitution rate matrix, standard errors, time taken, a reduced data set containing unique patterns and their frequencies, and model selection criteria values.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.6
Stability Stable
R(≥2.10), ape(≥3.2), testthat(≥0.9.1), Rcpp(≥0.11.4), numDeriv(≥2012.9.1), phangorn(≥1.99.13), knitr(≥1.10)
Maintained Yes


No version available



  • person_outline Dang U.J.

Publication for markophylo

markophylo institution(s)
Department of Biology, McMaster University, Hamilton, ON, Canada
markophylo funding source(s)
This work was supported by the National Sciences and Engineering Research Council of Canada [140221-10].

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