1.estimated Group restructuring rate of software FastEPRR (software download)
Download package FastEPRR.tar.gz, including FastEPRR_1.0.tar.gz (Linux/Unix installed version), FastEPRR_1.0.zip (Windows install version) and FastEPRR_manual.pdf (user manual).
Details of the group and the group of information can be accessed -
related information
Download package ItreeV.tar.gz, including Itree.jar (main program), ItreeV.bat (running under Windows file). ItreeV.sh (Linux / Unix run the file). ItreeV_manual.pdf manual.pdf (user manual). The examples folder (sample input) and readme file
CAMer package (Continuous Admixture Modeler) does Continuous Admixture Modeling (CAM) and related summary based on the result of MALDmef.
Related Publication: Modeling Continuous Admixture
1.Population model assumptions The population in each generation evolves following standard Wright Fisher model without mutation and selection. That is, randomly sample two individuals from the population, and randomly choose one of the chromosomes in each individual, pair and recombine them to form a new chromosome pair for the next generation. Repeat this process until sampling N chromosome pairs. Here N denotes population size in specific generation. Recombination is modeled as Poisson Process along the chromosome with rate 1 (Unit in Morgan).
2. AdmixSim description Here we implemented a very flexible simulator for admixed population, in which: 1) Can take arbitrary number of ancestral populations; 2) Can take arbitrary waves of population admixture; 3) Population size can be changed generation by generation; 4) And admixture proportions can also be changed generation by generation.
Currently, the Du program supports the fourpopularly used alignmentformat (ARLEQUIN, MEGA, NEXUS and PHYLIP). Please see the examples for the data format.
Related Publication: Statistical test for detecting recent positive selectionby partitioning coalescent tree (under publishing)