LoginSign Up
← Back to all sparks
E

EvoPhylo

ANALYTICS
Velocity0.0

Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics

github.com/tiago-simoes/EvoPhylo ↗

EvoPhylo added BEAST2 alongside MrBayes, then went quiet for two years.

phylogeneticsbayesian-inferencebeast2mrbayesresearch-software
◆Current state
EvoPhylo handles post-processing for Bayesian evolutionary rate and fossilized birth-death analyses, originally against MrBayes output. The 0.3.2 release added BEAST2 support for both FBD functions and rates analysis, making it usable by labs on either platform. Since then there has been one clock-partition fix and, in August 2025, a release whose notes say only that there are updated functions and bug fixes.
◆Where it's heading
The package's substantive arc ended with the 0.3.2 publication release, which arrived with peer-review revisions and three first-time contributors — the shape of software built to accompany a paper. What follows is thin: a MrBayes plotting correction in 0.3.3, then a two-year gap and a release with no described contents. The August 2025 entry may contain real work, but the notes give a reader nothing to judge.
◆Prediction
Without release notes on the latest version there is no observable basis for predicting the next move; the two-year gap before it suggests activity tied to specific research needs rather than a maintenance cadence.

◆Recent moves

  1. 11mo ago

    EvoPhylo v. 0.3.5

    A release described only as updated and new functions with some bug fixes — no specifics. It ends a two-year silence, but the notes make it impossible to tell whether anything here matters to existing users.

    View source ↗
  2. 3y ago

    EvoPhylo 0.3.3 fixes back-rate plots for MrBayes

    plot_back_rates() corrected for MrBayes output, with new warnings and handling for MrBayes single-clock partitions in plot_treerates_sgn(). Narrow follow-up work on the platform the package started with, shortly after BEAST2 support broadened it.

    View source ↗
  3. 3y ago

    EvoPhylo 0.3.2 adds BEAST2 support for FBD and rates

    The published release: BEAST2 handling for the fossilized birth-death functions and for rates analysis, plus support for trees with offset. A second inference engine rather than a new class of analysis, but it decides whether a lab can use the package at all.

    View source ↗