| T-LD |
Statistical estimator from LD |
Summary statistics of alignments scalable to genomic size |
LD of variants with genetic distance within 0.005–0.1 cM |
Point estimation |
Isolation–migration model |
| T-FST |
Statistical estimator from FST and LD |
Summary statistics of alignments scalable to genomic size |
LD of variants with genetic distance within 0.005–0.1 cM
SNP-wise FST of the two populations |
Point estimation |
Isolation–migration model |
| MIMAR |
MCMC |
Summary statistics at multiple neutral loci of size ~1000 bp |
The summary statistics at each locus: the numbers of polymorphisms unique to the samples from populations 1 and 2; the number of shared alleles between the two samples and the number of fixed alleles in either sample |
Posterior distribution mean±SD |
Isolation–migration model or more complex model specified by user |
| GPho |
MCMC |
Full data at multiple neutral loci of size ~1000 bp |
Each locus provides several samples of diploid or haploid sequences of multiple populations
Out-group sequence can be used for mutation rate calibration |
Posterior distribution mean±SD |
Phylogeny tree given by user
Constant population size to be estimated |
| DADI |
Diffusion approximation |
Summary statistics of alignments scalable to genomic size |
Allele frequency spectrum of multiple populations
Out-group information can be used for polarization |
Point estimation |
Demographic function specify by user with sets of parameters to be estimated |
| CoalHMM |
HMM–MCMC |
Full data of alignments scalable to genomic size |
Two genomic size haploid sequences: one from population_1 and the other one from population_2 |
Posterior distribution mean±SD |
Isolation model |
| PSMC |
HMM–maximize likelihood estimation |
Full data of alignments scalable to genomic size |
Pseudo-diploid sequences constructed from two genomic size haploid sequences: one from population_1 and the other one from population_2 |
Qualitative estimation. PSMC provides an estimation of historical population size as a step function of time. The time when population size tends to infinity is the divergence time |
A step function with boundaries of the intervals specified by users and function values to be estimated |
| MSMC |
HMM–maximize likelihood estimation |
Full data of alignments scalable to genomic size |
Small samples of genomic size phased sequences from two populations. Normally equal numbers of sequences in each of the two populations (2–4 haploid sequences for each population) |
Qualitative estimation. MSMC provides a metric, relative cross-coalescence rate to measures the gene exchange between two populations. It is a step function of time having value in [0,1]. It shows the dynamic process of relative gene flow changes between two populations, indicating the process of population divergence |
A step function with boundaries of the intervals specified by users and function values to be estimated |
