chum_populations

ryan.waples@gmail.com

####chum_populations

scripts
- contains python and R scripts for
data *
results
- batch_4
  - EIGENSOFT
  - ind_analysis
  - pop_analysis
  - synteny
linkage_map
plots
- flowcharts
- map
- popgen
- sequencing
- shiny
old

Name		Name	Last commit message	Last commit date
Latest commit History 184 Commits
.ipynb_checkpoints		.ipynb_checkpoints
data		data
linkage_map		linkage_map
old		old
paper		paper
plots		plots
results		results
scripts		scripts
.RData		.RData
.Rhistory		.Rhistory
.gitignore		.gitignore
.png		.png
.~lock.popmap#		.~lock.popmap#
Align to Chinook.ipynb		Align to Chinook.ipynb
CONFIG.ipynb		CONFIG.ipynb
Figures 6 & 7 .ipynb		Figures 6 & 7 .ipynb
LFMM dominance coding.ipynb		LFMM dominance coding.ipynb
LFMM.ipynb		LFMM.ipynb
Makefile		Makefile
Ne.ipynb		Ne.ipynb
Nucleotide diversity.ipynb		Nucleotide diversity.ipynb
PGDSpider-cli.log		PGDSpider-cli.log
Paper 1 map.ipynb		Paper 1 map.ipynb
README.md		README.md
Table1.ipynb		Table1.ipynb
Table2.ipynb		Table2.ipynb
TaqMan.ipynb		TaqMan.ipynb
Untitled.ipynb		Untitled.ipynb
align to salmo.ipynb		align to salmo.ipynb
align_pop_data_to_reference.ipynb		align_pop_data_to_reference.ipynb
assign_pop_genotypes.ipynb		assign_pop_genotypes.ipynb
bayescan.ipynb		bayescan.ipynb
bootstrap sample.ipynb		bootstrap sample.ipynb
chinook.1.bt2		chinook.1.bt2
chinook.2.bt2		chinook.2.bt2
chinook.3.bt2		chinook.3.bt2
chinook.4.bt2		chinook.4.bt2
chinook.rev.1.bt2		chinook.rev.1.bt2
chinook.rev.2.bt2		chinook.rev.2.bt2
chum_populations.Rproj		chum_populations.Rproj
construct_linkage_map.ipynb		construct_linkage_map.ipynb
convert_formats.ipynb		convert_formats.ipynb
coverage.ipynb		coverage.ipynb
draw map.ipynb		draw map.ipynb
file_tree.txt		file_tree.txt
filter_pop_genotypes.ipynb		filter_pop_genotypes.ipynb
freeBayes_notes.txt		freeBayes_notes.txt
generate_reference.ipynb		generate_reference.ipynb
genome scan.ipynb		genome scan.ipynb
genotype_families.ipynb		genotype_families.ipynb
informativeness of dominant markers.ipynb		informativeness of dominant markers.ipynb
legend.png		legend.png
mapped_non_paralogs_subset.log		mapped_non_paralogs_subset.log
multi-family mapping.ipynb		multi-family mapping.ipynb
pairwise Fst.ipynb		pairwise Fst.ipynb
phase parents.ipynb		phase parents.ipynb
place centromeres.ipynb		place centromeres.ipynb
plot_EIGENSTRAT.ipynb		plot_EIGENSTRAT.ipynb
plot_pop_genotypes.ipynb		plot_pop_genotypes.ipynb
plotting bayescan results.ipynb		plotting bayescan results.ipynb
popgen-individual.ipynb		popgen-individual.ipynb
popgen-populations.ipynb		popgen-populations.ipynb
population tree.ipynb		population tree.ipynb
run_EIGENSTRAT.ipynb		run_EIGENSTRAT.ipynb
salmonid species tree.ipynb		salmonid species tree.ipynb
todo.txt		todo.txt
tree.png		tree.png
workflow_outline.ipynb		workflow_outline.ipynb

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