Files in ruidlpm/pathPhynder

A workflow for integrating ancient lineages into present-day Y-chromosome phylogenies.

.gitignore

DESCRIPTION

LICENSE

R/Ympute.R R/Ympute2.R R/addAncToTree.R R/ancient_SNPs_to_branches.R R/assign_noNA.R R/chooseBestPath.R R/functions_pathPhynder.R R/make_vcf.R R/pathPhynder_likelihood_functions.R R/pathPhynder_likelihood_runner.R R/pileup_and_filter.R R/plot_likes.R R/prep_files.R R/prepare_sites_likelihood.R README.md

data/200803.snps_isogg.txt

data/210513.snps_isogg_curated.txt

data/210801.snps_isogg.b38.txt

data/211108.snps_isogg_curated.b38.txt

data/211108.snps_isogg_curated.txt

data/BigTree_Y/BigTree.Y.201219.grch38.treeIDs.vcf.gz

data/BigTree_Y/BigTree.Y.201219.grch38.treeIDs.vcf.gz.tbi

data/BigTree_Y/BigTree.Y.201219.vcf.gz

data/BigTree_Y/BigTree.Y.201219.vcf.gz.tbi

data/BigTree_Y/bigtree_annotated_V1.nwk

data/BigTree_Y/bigtree_branches.snp.gz

data/badsnps.txt

data/hap_order.txt

data/mismatchsnps.txt

data/reference_sequences/GRCH38.p12_Y.fa.gz

data/reference_sequences/GRCH38.p12_Y.fa.gz.fai

data/reference_sequences/GRCH38.p12_Y.fa.gz.gzi

data/reference_sequences/hg19_chrY.fa.gz

data/reference_sequences/hg19_chrY.fa.gz.fai

data/reference_sequences/hg19_chrY.fa.gz.gzi

data/reference_sequences/hs37d5_Y.fa.fai

data/reference_sequences/hs37d5_Y.fa.gz

data/reference_sequences/hs37d5_Y.fa.gz.fai

data/reference_sequences/hs37d5_Y.fa.gz.gzi

data/reference_sequences/mtDNA.fa.gz

data/reference_sequences/mtDNA.fa.gz.fai

data/reference_sequences/mtDNA.fa.gz.gzi

data/reference_sequences/rCRS_NC.fa.gz

data/reference_sequences/rCRS_NC.fa.gz.fai

data/reference_sequences/rCRS_NC.fa.gz.gzi

data/remove_badSNPs.R figures/workflow.pdf

figures/workflow.png

inst/python/call_bases_chrY_v2.1.py

pathPhynder.R tutorial/README.md

ruidlpm/pathPhynder documentation built on June 13, 2022, 2:15 p.m.