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References from Genetic Diversity and Selection Signatures of Three Indonesian Indigenous Pig Populations From Eastern Indonesia Using Whole Genome Sequencing Data. Local targets link to admitted publications; unresolved targets remain external evidence.
Fast Model‐Based Estimation of Ancestry in Unrelated Individuals
10.1101/gr.094052.109 · 2009 · External reference
Unresolved reference
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Genetic Diversity and Relationship of Indonesian Indigenous Chickens Inferred From Microsatellite DNA Markers
10.4038/tar.v26i4.8126 · 2015 · External reference
Unresolved reference
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Trimmomatic: A Flexible Trimmer for Illumina Sequence Data
10.1093/bioinformatics/btu170 · 2014 · External reference
10.1186/1471‐2156‐15‐85
10.1186/1471‐2156‐15‐85 · External reference
A Program for Annotating and Predicting the Effects of Single Nucleotide Polymorphisms, SnpEff: SNPs in the Genome of Drosophila melanogaster Strain w1118; Iso‐2; Iso‐3
10.4161/fly.19695 · 2012 · External reference
The Variant Call Format and VCFtools
10.1093/bioinformatics/btr330 · 2011 · External reference
Candidate Genes Related to Growth and Milk Production in Three Anatolian Goats Revealed by GWAS
2026 · External reference
A Molecular Marker of Milk Composition Traits in NCAM2 Gene of Chinese Holstein
10.1080/10495398.2020.1772802 · 2022 · External reference
Ancestral Alleles Defined for 70 Million Cattle Variants Using a Population‐Based Likelihood Ratio Test
10.1186/s12711-024-00879-6 · 2024 · External reference
The 1000 Chinese Indigenous Pig Genomes Project Provides Insights Into the Genomic Architecture of Pigs
2024 · External reference
Deciphering Genetic Characteristics of South China and North China Indigenous Pigs Through Selection Signatures
10.1186/s12864-024-11119-y · 2024 · External reference
Rehh : An R Package to Detect Footprints of Selection in Genome‐Wide SNP Data From Haplotype Structure
10.1093/bioinformatics/bts115 · 2012 · External reference
Whole‐Genome Resequencing Reveals Genetic Differentiation and Selection Signatures Among Wild, Local and Commercial Duck Populations
10.5713/ab.24.0643 · 2025 · External reference
Genetic Signatures Reveal High‐Altitude Adaptation in a Set of Ethiopian Populations
10.1093/molbev/mst089 · 2013 · External reference
The Evolution and Role of Molecular Tools in Measuring Diversity and Genomic Selection in Livestock Populations (Traditional and up‐To‐Date Insights): A Comprehensive Exploration
10.3390/vetsci11120627 · 2024 · External reference
The Impact of Using Different Ancestral Reference Populations in Assessing Crossbred Population Admixture and Influence on Performance
10.3389/fgene.2022.910998 · 2022 · External reference
Selection for Complex Traits Leaves Little or no Classic Signatures of Selection
10.1186/1471-2164-15-246 · 2014 · External reference
The Genome Landscape of Indigenous African Cattle
2017 · External reference
Unresolved reference
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Pixy: Unbiased Estimation of Nucleotide Diversity and Divergence in the Presence of Missing Data
10.1111/1755-0998.13326 · 2021 · External reference
Variation in Breeding Practices and Geographic Isolation Drive Subpopulation Differentiation, Contributing to the Loss of Genetic Diversity Within Dog Breed Lineages
10.1186/s40575-020-00085-9 · 2020 · External reference
Phylogeny and Ancient DNA of Sus Provides Insights Into Neolithic Expansion in Island Southeast Asia and Oceania
10.1073/pnas.0607753104 · 2007 · External reference
Germplasm of Indonesia Local Pig: Potential, Threat of Extinction, and Conservation Strategy
2024 · External reference
FastME 2.0: A Comprehensive, Accurate, and Fast Distance‐Based Phylogeny Inference Program
10.1093/molbev/msv150 · 2015 · External reference
Characterization Analysis of Rongchang Pig Population Based on the Zhongxin‐1 Porcine Breeding Array PLUS
10.5713/ab.23.0049 · 2023 · External reference
Interactive Tree of Life (iTOL) v6: Recent Updates to the Phylogenetic Tree Display and Annotation Tool
10.1093/nar/gkae268 · 2024 · External reference
Unresolved reference
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The Sequence Alignment/Map Format and SAMtools
10.1093/bioinformatics/btp352 · 2009 · External reference
Revealing Genetic Diversity and Population Structure of Endangered Altay White‐Headed Cattle Population Using 100 k SNP Markers
10.3390/ani12223214 · 2022 · External reference
Detection of Selection Signatures in Farmed Coho Salmon ( Oncorhynchus kisutch ) Using Dense Genome‐Wide Information
10.1038/s41598-021-86154-w · 2021 · External reference
Genetic Diversity in Global Chicken Breeds in Relation to Their Genetic Distances to Wild Populations
10.1186/s12711-021-00628-z · 2021 · External reference
The Genome Analysis Toolkit: A MapReduce Framework for Analyzing Next‐Generation DNA Sequencing Data
10.1101/gr.107524.110 · 2010 · External reference
Investigating Genetic Diversity of Indonesian Native Cattle Breeds Using mitochondrialDNA 16S rRNA Gene
10.55730/1300-0128.4216 · 2022 · External reference
NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data
10.1371/journal.pone.0030619 · 2012 · External reference
PLINK: A Tool Set for Whole‐Genome Association and Population‐Based Linkage Analyses
10.1086/519795 · 2007 · External reference
Application of Site and Haplotype‐Frequency Based Approaches for Detecting Selection Signatures in Cattle
10.1186/1471-2164-12-318 · 2011 · External reference
Decoding the Molecular Landscape of Prepubertal Oocyte Maturation: GTPBP4 as a Key Driver of in Vitro Developmental Competence
10.1111/cpr.70017 · 2025 · External reference
Uncovering Genomic Diversity and Signatures of Selection in Red Angus × Chinese Red Steppe Crossbred Cattle Population
10.1038/s41598-025-98346-9 · 2025 · External reference
Unbiased Population Heterozygosity Estimates From Genome‐Wide Sequence Data
10.1111/2041-210x.13659 · 2021 · External reference
Unresolved reference
2014 · External reference
Whole Genome Mapping Reveals Novel Genes and Pathways Involved in Milk Production Under Heat Stress in US Holstein Cows
10.3389/fgene.2019.00928 · 2019 · External reference
Unresolved reference
1997 · External reference
Pengembangan Ternak Babi Lokal di Indonesia
2015 · External reference
F‐Box Only Protein (FBXO) Family Genes in Cattle ( Bos taurus ): Genome‐Wide Identification and Functions in the Skeletal Muscle Development
10.1016/j.ygeno.2025.111127 · 2025 · External reference
Haplotype and Phylogenetic Diversity Using Mitochondrial 12S rRNA Gene Marker in Bali Cattle
10.14710/jitaa.48.3.169-181 · 2023 · External reference
Genome‐Wide Analyses Reveal Genetic Convergence of Prolificacy Between Goats and Sheep
10.3390/genes12040480 · 2021 · External reference
Unresolved reference
1995 · External reference
A Map of Recent Positive Selection in the Human Genome
10.1371/journal.pbio.0040072 · 2006 · External reference
Unresolved reference
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Marker‐Based Estimates of Relatedness and Inbreeding Coefficients: An Assessment of Current Methods
10.1111/jeb.12315 · 2014 · External reference
VCF2Dis: An Ultra‐Fast and Efficient Tool to Calculate Pairwise Genetic Distance and Construct Population Phylogeny From VCF Files
2025 · External reference
GCTA: A Tool for Genome‐Wide Complex Trait Analysis
10.1016/j.ajhg.2010.11.011 · 2011 · External reference
Genetic Diversity and Population Structure of Tongcheng Pigs in China Using Whole‐Genome SNP Chip
10.3389/fgene.2022.910521 · 2022 · External reference
Implications for the Use of Horse Hair Roots as a DNA Source for Microsatellite Typing
10.17221/4254-cjas · 2005 · External reference
Microsatellite Markers Developed Based on Transcriptomic Data Reveal the Genetic Diversity and Population Genetic Structure of Angulyagra Polyzonata in Guangxi, China
10.3390/biology14101424 · 2025 · External reference
A High‐Performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
10.1093/bioinformatics/bts606 · 2012 · External reference
