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ABBA_BABA_Fernando
ABBA_BABA_Fernando
 
 
Cassiope_tetragona_genome
Cassiope_tetragona_genome
 
 
Fernando_SFS_plots
Fernando_SFS_plots
 
 
Figures_data
Figures_data
 
 
GBS_barcodes
GBS_barcodes
 
 
Mimulus
Mimulus
 
 
fastsimcoal2
fastsimcoal2
 
 
.gitattributes
.gitattributes
 
 
.gitignore
.gitignore
 
 
Notes0_Mar2023_Coverage_RefOpt_Feb2023.bash
Notes0_Mar2023_Coverage_RefOpt_Feb2023.bash
 
 
Notes1_Mar2023_Demultiplex_dDocent_Mar2023.bash
Notes1_Mar2023_Demultiplex_dDocent_Mar2023.bash
 
 
Notes2_Mar2023_SNP_filtering_Plink_Admixture.txt
Notes2_Mar2023_SNP_filtering_Plink_Admixture.txt
 
 
Notes3_Mar2023_PopStats_SplitsTree.txt
Notes3_Mar2023_PopStats_SplitsTree.txt
 
 
Notes4_Mar2023_ABBA_BABA.txt
Notes4_Mar2023_ABBA_BABA.txt
 
 
Notes5_Mar2023_Rplots_Admix5groups_PCA_PopStats.R
Notes5_Mar2023_Rplots_Admix5groups_PCA_PopStats.R
 
 
Notes6_Mar2023_Rplots_Fst_Mantel_Distance.R
Notes6_Mar2023_Rplots_Fst_Mantel_Distance.R
 
 
Notes7a_Mar2023_Treemix.txt
Notes7a_Mar2023_Treemix.txt
 
 
Notes7b_Mar2023_Treemix_plots.R
Notes7b_Mar2023_Treemix_plots.R
 
 
Notes8a_Mar2023_fastsimcoal2.bash
Notes8a_Mar2023_fastsimcoal2.bash
 
 
Notes8a_Mar2024_fastsimcoal2.bash
Notes8a_Mar2024_fastsimcoal2.bash
 
 
Notes8a_Nov2023_fastsimcoal2.bash
Notes8a_Nov2023_fastsimcoal2.bash
 
 
Notes8b_Mar2023_dadi_plotting.py
Notes8b_Mar2023_dadi_plotting.py
 
 
Notes8c_Mar2023_fastsimcoal2_plotting.R
Notes8c_Mar2023_fastsimcoal2_plotting.R
 
 
Notes9_Mar2023_Ancient_DNA_BLAST.txt
Notes9_Mar2023_Ancient_DNA_BLAST.txt
 
 
Notes_upload_to_Genbank.txt
Notes_upload_to_Genbank.txt
 
 
Population_genomics_Cassiope.Rproj
Population_genomics_Cassiope.Rproj
 
 
README.md
README.md
 
 
dDocent lab blog_dDocent install_tmux sessions.docx
dDocent lab blog_dDocent install_tmux sessions.docx
 
 

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Population_genomics_Cassiope

Step by step notes for analyzing the GBS data from 40 circumpolar populations of Cassiope tetragona
Written to be run on Cedar Compute Canada, file/pathnames etc. will need to be edited throughout to run on other data

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Step by step notes for analyzing the GBS data from 40 circumpolar populations of Cassiope tetragona

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