PAPipe result browser

Principal component analysis by GCTA

Parameters

Server path: ./04_Population//29-11-2023_15:37:36/PCA/all.PCA.pdf

Local path: [Local_web directory path]/04_Population/29-11-2023_15:37:36/PCA/all.PCA.pdf

Phylogenetic analysis

Parameters

Server path: ./04_Population//29-11-2023_15:37:36/PhylogeneticTree/

Local path: [Local_web directory path]/04_Population/29-11-2023_15:37:36/PhylogeneticTree/

Newick Tree

Population structure analysis

Parameters

Server path: ./04_Population//29-11-2023_15:37:36/Structure/CLUMPAK/job_100_pipeline_summary.pdf

Local path: [Local_web directory path]/04_Population/29-11-2023_15:37:36/Structure/CLUMPAK/job_100_pipeline_summary.pdf

Fixation index analysis

Parameters

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Angus_VS_rest_all_populations/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Angus_VS_rest_all_populations/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Hanwoo_VS_rest_all_populations/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Hanwoo_VS_rest_all_populations/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Holstein_VS_rest_all_populations/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Holstein_VS_rest_all_populations/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Jersey_VS_rest_all_populations/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Jersey_VS_rest_all_populations/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Simmental_VS_rest_all_populations/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Simmental_VS_rest_all_populations/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Angus_VS_Hanwoo/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Angus_VS_Hanwoo/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Angus_VS_Holstein/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Angus_VS_Holstein/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Angus_VS_Jersey/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Angus_VS_Jersey/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Angus_VS_Simmental/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Angus_VS_Simmental/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Hanwoo_VS_Holstein/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Hanwoo_VS_Holstein/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Hanwoo_VS_Jersey/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Hanwoo_VS_Jersey/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Hanwoo_VS_Simmental/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Hanwoo_VS_Simmental/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Holstein_VS_Jersey/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Holstein_VS_Jersey/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Holstein_VS_Simmental/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Holstein_VS_Simmental/Fst_result.pdf

Server path: ./04_Population//29-11-2023_15:37:36/Fst/Jersey_VS_Simmental/Fst_result.pdf

Local path: [Local_web directory path]/04_Population/Fst/Jersey_VS_Simmental/Fst_result.pdf

Pairwise sequentially Markovian coalescent analysis

Parameters

Server path: ./04_Population//29-11-2023_15:37:36/EffectiveSize/psmc_plot.pdf

Local path: [Local_web directory path]/04_Population/29-11-2023_15:37:36/EffectiveSize/psmc_plot.pdf

Population admixture analysis

Parameters

Server path: ./04_Population//29-11-2023_15:37:36/AdmixtureProportion/admixtools_3pop/3pop.out

Local path: [Local_web directory path]/04_Population/AdmixtureProportion/admixtools_3pop/3pop.out

Server path: ./04_Population//29-11-2023_15:37:36/AdmixtureProportion/admixtools_4diff/4diff.out

Local path: [Local_web directory path]/04_Population/AdmixtureProportion/admixtools_4diff/4diff.out

Server path: ./04_Population//29-11-2023_15:37:36/AdmixtureProportion/admixtools_Dstat/Dstat.out

Local path: [Local_web directory path]/04_Population/AdmixtureProportion/admixtools_Dstat/Dstat.out

Server path: ./04_Population//29-11-2023_15:37:36/AdmixtureProportion/admixtools_f4stat/f4stat.out

Local path: [Local_web directory path]/04_Population/AdmixtureProportion/admixtools_f4stat/f4stat.out

Linkage disequilibrium decay analysis

Parameters

Server path: ./04_Population//29-11-2023_15:37:36/LdDecay/500//Plot/out.pdf

Local path: [Local_web directory path]/04_Population/LdDecay/500//Plot/out.pdf

Server path: ./04_Population//29-11-2023_15:37:36/LdDecay/1000//Plot/out.pdf

Local path: [Local_web directory path]/04_Population/LdDecay/1000//Plot/out.pdf

Server path: ./04_Population//29-11-2023_15:37:36/LdDecay/5000//Plot/out.pdf

Local path: [Local_web directory path]/04_Population/LdDecay/5000//Plot/out.pdf

Server path: ./04_Population//29-11-2023_15:37:36/LdDecay/10000//Plot/out.pdf

Local path: [Local_web directory path]/04_Population/LdDecay/10000//Plot/out.pdf

Multiple sequentially Markovian coalescent analysis

Parameters

Server path: ./04_Population//29-11-2023_15:37:36/MSMC/MSMC.pdf

Local path: [Local_web directory path]/04_Population/29-11-2023_15:37:36/MSMC/MSMC.pdf

Selective sweep analysis

Parameters

Server path: ./04_Population//29-11-2023_15:37:36/SweepFinder2/Holstein/SweepFinderOut.pdf

Local path: [Local_web directory path]/04_Population/SweepFinder2/Holstein/SweepFinderOut.pdf

Server path: ./04_Population//29-11-2023_15:37:36/SweepFinder2/Simmental/SweepFinderOut.pdf

Local path: [Local_web directory path]/04_Population/SweepFinder2/Simmental/SweepFinderOut.pdf

Server path: ./04_Population//29-11-2023_15:37:36/SweepFinder2/Jersey/SweepFinderOut.pdf

Local path: [Local_web directory path]/04_Population/SweepFinder2/Jersey/SweepFinderOut.pdf

Server path: ./04_Population//29-11-2023_15:37:36/SweepFinder2/Angus/SweepFinderOut.pdf

Local path: [Local_web directory path]/04_Population/SweepFinder2/Angus/SweepFinderOut.pdf

Server path: ./04_Population//29-11-2023_15:37:36/SweepFinder2/Hanwoo/SweepFinderOut.pdf

Local path: [Local_web directory path]/04_Population/SweepFinder2/Hanwoo/SweepFinderOut.pdf

Principal component analysis by PLINK v 2.0

Parameters

Server path: ./04_Population//29-11-2023_15:37:36/Plink2/PCA_projection.pdf

Local path: [Local_web directory path]/04_Population/29-11-2023_15:37:36/Plink2/PCA_projection.pdf

Population tree analysis

Parameters

Server path: ./04_Population//29-11-2023_15:37:36/Treemix/Treemix.results.pdf

Local path: [Local_web directory path]/04_Population/29-11-2023_15:37:36/Treemix/Treemix.results.pdf

Visualization of the analysis results by PAPipe

Principal component analysis by GCTA

Phylogenetic analysis

Population structure analysis

Fixation index analysis

Pairwise sequentially Markovian coalescent analysis

Population admixture analysis

Linkage disequilibrium decay analysis

Multiple sequentially Markovian coalescent analysis

Selective sweep analysis

Principal component analysis by PLINK v 2.0

Population tree analysis