iMAAPs Version 1
iMAAPs is a powerful tool to estimate multiple-wave population admixed time, which is currently designed to infer the two-way, multiple-wave admixture based on admixture induced LD. This software can deal with genotype data, haplotype data and the data re-coded according to admixture ancestries
Input Parameters
How to cite
Zhou Y, Yuan K, Yu Y, Ni X, Xie P, Xing EP, Xu S. Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions[J]. Heredity, 2017, 118(5):503. [PMID=28198814]
Help information

Version 1

Usage: -name -ind_file -Refpops -Timefile -Jackknife -Mindis -Maxdis -Binsize -Iter -Num_threads -geno -snp


-name                  Sample name.

-ind_file               Individual notation.

-Refpops            Labels for reference populations.

-Timefile               Time file for testing the admixture signals.

-Jackknife              Whether applied jack knife test.[off]("1" "on"  "ON"  stands for OPEN. "0" "off" "OFF" stands for CLOSE.)

-Mindis                 Minimum distance of two WLD bins(in Morgan).[0.0002]

-Maxdis                 Maximum distance of two WLD bins(in Morgan).[0.3]

-Binsize                Bin size of WLD bin(in Morgan).[0.0002]

-Iter                   Number of iteration to the final fitting results.[100000]

-Num_threads            Number of threads used globally.[1]

-geno                  List of genotype files.(",")

-snp                   List of snp files.(",")

Parameters Description
-S: Sample name
sample name.
-I: Ind file
individual notation.
-R: Refpops
labels for reference populations.(separated by commas, such as POP1,POP2)
-T: Timefile
time file for testing the admixture signals.
-J: Jackknife
whether applied jack knife test.[off]("1" "on"  "ON"  stands for OPEN. "0" "off" "OFF" stands for CLOSE.)
-Min: Mindis
minimum distance of two WLD bins(in Morgan).
-Max: Maxdis
maximum distance of two WLD bins(in Morgan).
-B: Binsize
bin size of WLD bin(in Morgan).
-Iter: Iter
number of iteration to the final fitting results.
-N: Num_threads
number of threads used globally.
-G: Geno
list of genotype files.(",")
list of snp files.(",")