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maxaltall  

'FASTA' ML and ‘altall’ Sequences from IQ-TREE .state Files
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("maxaltall", "0.1.0")



Attach the package and use:
library("maxaltall")
Maintained by
Philip D. Kiser
[Scholar Profile | Author Map]
First Published: 2024-09-25
Latest Update: 2024-09-25
Description:
Takes a .state file generated by IQ-TREE as an input and, for each ancestral node present in the file, generates a FASTA-formatted maximum likelihood (ML) sequence as well as an ‘AltAll’ sequence in which uncertain sites, determined by the two parameters thres_1 and thres_2, have the maximum likelihood state swapped with the next most likely state as described in Geeta N. Eick, Jamie T. Bridgham, Douglas P. Anderson, Michael J. Harms, and Joseph W. Thornton (2017), "Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty" <doi:10.1093/molbev/msw223>.
How to cite:
Philip D. Kiser (2024). maxaltall: 'FASTA' ML and ‘altall’ Sequences from IQ-TREE .state Files. R package version 0.1.0, https://cran.r-project.org/web/packages/maxaltall. Accessed 02 Apr. 2025.
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