1) MFDM software 1.1 (download, document)

To detect recent positive selection reliably in natural populations.

Deprecated old version: MFDM software 1.0 (download, document)

2) R package: evolBoosting 1.0.1 ( windows, unix, document )

To detect positive selection by combining different summary statistics.
evolBoosting 1.0.1 was updated on 2016-5-26: rebuilt with R version 3.2.5.

Depracated old version: evolBoosting 1.0.0 (windows, unix, document): built with R version 2.15.0.

3) msmfs (download, readme)

msmfs is modified Hudson's ms simulator. It can generate simulation data under the condition of compact folded mutation frequency spectrum, missing data or multiple hits.

4) FastEPRR (download)

An extremely fast open-source software package to estimate population recombination rate based on intraspecific DNA polymorphism data.

5) Du package (windows, unix, readme)

A single locus test for detecting recent positive selection by bi-partitioning the coalescent tree. (submitted)

6) eGPS (Windows, Ubuntu, MAC OS, tutorials,TestData)

eGPS standalone software is a multi-functional evolutionary and genomic analysis desktop software. Now it can deal with VCF, multiple sequence alignment, protein-omics files and so on. Its functionality includes building,viewing and modifying phylogenetic tree; analyzing VCF files; viewing circular RNA results; performing coalescent simulation under user constructed demographic model; analyzing protein-omics data to get differentially expressed genes and so on. Especially, with the support of eGPS cloud and other open-online resources, it provides one-click to get gene tree from candidate genes.

7) NeutralityTest version1.2 (zipped format, exe format, help)

8) KungFuPanda (KungFuPanda, Manual)

The KungFuPanda is a program for examination of accelerated evolution. The software was written in Java and suitable for different computer platform. It was designed for both of the high performance computing environment, such as computer cluster, and a personal computer. The software can analyze the accelerated evolution of an internal branch in a user-defined tree, based on a user-defined configure file.
















Group of Evolutionary Genomics, PICB