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Table 2 Statistical methods applied in Y-LineageTracker

From: Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data

Function

Method or Statistics

Reference

Clustering Analysis

Principal component analysis (PCA)

[23]

Multidimensional scaling (MDS)

[24, 25]

Phylogeny Analysis

Maximum parsimony (MP)

[26, 27]

Identity by state (IBS)

[28, 29]

Network Analysis

Median-joining (MJ)

[30]

Statistical Analysis

Haplotype diversity (HD)

[31]

Mean pairwise distance (MPD)

[32]

Fixation index (Fst)

[33]

Genetic diversity (Gst)

[34, 35]

Analysis of molecular variance (AMOVA)

[36]

Haplogroup prediction from Y-STRs

[37]

Time Estimation

Mcmctree in PAML

[21]

Rho statistics

[38]

The average squared difference (ASD)

[39, 40]

  1. The published Y-DNA analysis methods applied in Y-LineageTracker