# YR-MPE
**Repository Path**: ZJXMolls/YR-MPE
## Basic Information
- **Project Name**: YR-MPE
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: GPL-3.0
- **Default Branch**: main
- **Homepage**: None
- **GVP Project**: No
## Statistics
- **Stars**: 0
- **Forks**: 0
- **Created**: 2026-02-08
- **Last Updated**: 2026-04-30
## Categories & Tags
**Categories**: Uncategorized
**Tags**: None
## README
# YR-MPE - Molecular Phylogenetics & Evolution Plugins for YRTools
[](https://www.python.org/downloads/)
[](LICENSE)
[]()
[](https://deepwiki.com/Gipsy-The-Sheller/YR-MPE)
> [!NOTE]
>
> If you find this repository useful for your research, please consider giving it a star! It helps me gauge interest. For any questions, please open an issue.
>
> If you want a specific function, please describe it in detail in a new issue. I will consider implementing it in priority.
>
> YR-MPE temporarily have no publications. If you need to cite it, please cite the repository.
## Graphic Overview of all features
|Analysis|Figure|Children|Figure|
|:---|:---|:---|:---|
| Data Management | 
| SeqMatrix
SeqDBG
Sequence Concatenator
TreeMerger |
|
| Align |
| Clustal Omega
MAFFT
Muscle 5
MACSE | |
| Trim |
| TrimAl
GBlocks | |
| Model |
| ModelFinder | 
|
| Distance |
| ML-distance (IQ-Tree 3)
Uncorrected distance | 
|
| Phylogeny |
| IQ-Tree 3
MrBayes3-MPI-BEAGLE3
PhyloBayes-MPI
DecentTree (NJ methods)
MPBoot (Maximum Parsimony)
CASTER-site
ASTRAL|
|
| Visualizations ||Sequence Viewer
Distance Visualization
Calculate & Plot Substitution Satucation
MiniTracer
IcyTree|
|
| Platform & Workflow | | YR-MPEA | |
## What is YR-MPE?
`YR-MPE` is originally a collection of plugins for `YRTools`, which is a plugin-based bioinformatic platform. `YR-MPE` is for its molecular phylogenetics and evolution analysis functions.
While other software also provides good experience, an inherent conflict is the gap between these integrative software's good experience and most up-to-date functions, since computational molecular evolution is developed at a rapid pace.
Owing to a good architecture, the source codes of `YR-MPE` do not need any compilation or packaging, even without a global python environment. Thus, every new commit can be a new release, supporting speedy updates directly from Github repository. Also, it is open-sourced, which means you can modify it as you wish, and community can develop new functions in collaboration. As a result, I think `YR-MPE` is capable to keep up with the development of the discipline.
> [!IMPORTANT]
>
> Most users requiring a good graphic interface experience are not bioinformatic-backgrounded and linux CLI novices, as observed by the developers. However, most software are only with mature buuild support on UNIX-like systems and are hard to successfully compile on Windows, which is disturbing to the focus on biological questions. YR-MPE is with the concept that developers form a stable x86_64 Windows building support once and for all, and everyone share the benefits. Till now there are several tools with YR-MPE the only known support on x86_64 Windows system:
> |Software|Feature|
> |:---|:---|
> | MrBayes-MPI-BEAGLE | The first stable MPI and BEAGLE3 support of MrBayes on Windows, speeding up 3x-7x for a 20 taxa, 1000 bp dataset (based on our benchmarks).|
> | PhyloBayes-MPI | The first stable MPI support of PhyloBayes on Windows. |
> | MPBoot | The first public release on Windows. |
> | DecentTree | The first public release on Windows. |
> | RaxML-NG (implementation planned) | The first public release on Windows |
>
> All binaries compiled by the authors, plus source codes, configuration and building files, are deposited in [this repository](https://github.com/Gipsy-The-Sheller/YR-MPE-Windows-x86_64-softwares) and distributed with their original licenses.
## How to use it?
You can invoke all or part of `YR-MPE` from any UI software (or even a python script) in `PyQt5` ecology.
The most convenient way is to use it in `YRTools` [Github](https://github.com/Gipsy-The-Sheller/YRTools) [Gitee-coming out soon](). You can get the up-to-date version direct from repository on click with its package manager `YR-Pacman`.
The wiki of `YR-MPE` provides detailed introduction and usage. You can access its [Github](https://github.com/Gipsy-The-Sheller/YR-MPE/wiki) or [Gitee](https://gitee.com/ZJXMolls/YR-MPE/wikis) source online.
## The development plan for next versions
- Integrate RAxML-NG
- Integrate Terraphast for phylogenetic terrace analysis
- Enable Robinson-Fould (RF) distance calculation
- Enable general majority-rule consensus for raw tree sets
- Integrate TreeRecs for gene tree confliction viz.
- Implement a molecular clock diagnosis (based on 2-cluster test or beanch length test) plugin interface
- Integrate MCMCTree and r8s
- Implement a fast distance calculation (JC69; poisson; K2P) and distance tree construction plugin with Biopython
- New dataset creator based on Orthofinder (for orthologs) and SibeliaZ (for collinear blocks)
- Do you think it is a need to integrate TreeMix?
- Or it is a need to implement a sequence simulator interface (based on AliSim implemented in IQ-Tree)?
Inform developers of your opinion via issue or email: zjxmolls@outlook.com.
## Changelogs
> *First transplant release on x86_64 windows
**Latest version: 2026.3.8 - v0.3.0 - Support for multigene phylogeny; distance methods (DecentTree\*); maximum parsimony (MPBoot\*); molecular dating (LSD2, MrBayes); nucleotide substitution saturation analysis (BaCoCa C-value reimplement); model parameter estimation (ModelFinder); dataset management (SeqDBG); uncalibrated distance (p-distance) calculation.**
2026.1.9 - v0.2.0 - Bayesian inference plugins (MrBayes-MPI-BEAGLE3\*, PhyloBayes-MPI\*), fixed IcyTree bugs, added console plugin.