Other packages > Find by keyword >

markophylo  

Markov Chain Models for Phylogenetic Trees
View on CRAN: Click here


Download and install markophylo package within the R console
Install from CRAN:
install.packages("markophylo")

Install from Github:
library("remotes")
install_github("cran/markophylo")

Install by package version:
library("remotes")
install_version("markophylo", "1.0.9")



Attach the package and use:
library("markophylo")
Maintained by
Utkarsh J. Dang
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-07-07
Latest Update: 2023-09-19
Description:
Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data. Examples of such discrete character data include restriction sites, gene family presence/absence, intron presence/absence, and gene family size data. Hypothesis-driven user- specified substitution rate matrices can be estimated. Allows for biologically realistic models combining constrained substitution rate matrices, site rate variation, site partitioning, branch-specific rates, allowing for non-stationary prior root probabilities, correcting for sampling bias, etc. See Dang and Golding (2016) for more details.
How to cite:
Utkarsh J. Dang (2015). markophylo: Markov Chain Models for Phylogenetic Trees. R package version 1.0.9, https://cran.r-project.org/web/packages/markophylo. Accessed 17 Jul. 2026.
Previous versions and publish date:
(2026-07-09 06:28), 1.0.1 (2015-07-07 18:11), 1.0.2 (2015-08-31 23:34), 1.0.3 (2015-11-06 01:09), 1.0.4 (2015-12-31 08:29), 1.0.6 (2018-01-30 18:14), 1.0.7 (2019-03-22 16:00), 1.0.8 (2020-07-05 19:40)
Other packages that cited markophylo R package
View markophylo citation profile
Other R packages that markophylo depends, imports, suggests or enhances
Complete documentation for markophylo
Functions, R codes and Examples using the markophylo R package
Some associated functions: estimaterates . estimaterates_f . markophylo-package . patterns . plottree . print.markophylo . simdata1 . 
Some associated R codes: RcppExports.R . custom-general14.R . estimatesrates_f.R .  Full markophylo package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

VFS  
Vegetated Filter Strip and Erosion Model
Empirical models for runoff, erosion, and phosphorus loss across a vegetated filter strip, given sl ...
Download / Learn more Package Citations See dependency  
alabama  
Constrained Nonlinear Optimization
Augmented Lagrangian Adaptive Barrier Minimization Algorithm for optimizing smooth nonlinear object ...
Download / Learn more Package Citations See dependency  
VEwaningVariant  
Vaccine Efficacy Over Time - Variant Aware
Implements methods for inference on potential waning of vaccine efficacy and for estimation of vacci ...
Download / Learn more Package Citations See dependency  
FastKNN  
Fast k-Nearest Neighbors
Compute labels for a test set according to the k-Nearest Neighbors classification. This is a fast wa ...
Download / Learn more Package Citations See dependency  
rt.test  
Robustified t-Test
Performs one-sample t-test based on robustified statistics using median/MAD (TA) and Hodges-Lehmann/ ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  

27,806

R Packages

239,283

Dependencies

73,837

Author Associations

27,807

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA