Explore Temporal and Other Phylogenetic Signals

Sequences sampled at different time points can be used to infer molecular phylogenies on natural time scales, but if the sequences records inaccurate sampling times, that are not the actual sampling times, then it will affect the molecular phylogenetic analysis. This shiny application helps exploring temporal characteristics of the evolutionary trees through linear regression analysis and with the ability to identify and remove incorrect labels. The method was extended to support exploring other phylogenetic signals under strict and relaxed models.

shinyTempSignal: Explore Temporal and Other Phylogenetic Signals

Sequences sampled at different time points can be used to infer molecular phylogenies on natural time scales, but if the sequences records inaccurate sampling times, that are not the actual sampling times, then it will affect the molecular phylogenetic analysis. This shiny application helps exploring temporal characteristics of the evolutionary trees through linear regression analysis and with the ability to identify and remove incorrect labels. The method was extended to support exploring other phylogenetic signals under strict and relaxed models.

If you use shinyTempSignal, please cite:

L Zhan, X Luo, W Xie, XA Zhu, Z Xie, J Lin, L Li, W Tang, R Wang, L Deng, Y Liao, B Liu, Y Cai, Q Wang, S Xu, G Yu. shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals. Journal of Genetics and Genomics 2024. doi: 10.1016/j.jgg.2024.02.004

:writing_hand: Authors

YuLab@SMU https://yulab-smu.top

Installation

# to install cran version
install.packages("shinyTempSignal")

# to install github version
if(!require("remotes")) install.packages("remotes")

remotes::install_github("YuLab-SMU/shinyTempSignal")

Usages

library(shinyTempSignal)
run_shinyTempSignal()