TRACE Data Resources

This repository is meant to contain the primary tables and data resources for recreating the primary figures in the following manuscript:

Recovering signatures of archaic hominin introgression using ancestral recombination graphs.
Yulin Zhang, Arjun Biddanda, Sarah A. Johnson, Colm O’Dushlaine, Priya Moorjani
bioRxiv 2026.03.03.709416; doi: https://doi.org/10.64898/2026.03.03.709416

## Git Repos

trace: This repo contains pip installable versions of TRACE algorithm

https://github.com/YulinZhang9806/trace.git

trace_paper: This repo contains analysis pipelines applied in the paper

https://github.com/YulinZhang9806/trace_paper.git

### `tables` 

These consist of post-processed tables of archaic tract calls from the manuscript across all tested populations.

The *t_number* in the filenames indicates the value of `t` used when running `trace-extract` to assign the focal branch timescale.

`trace_t31500_den.csv` recorded inference results for super-archaic segments within Denisovan segments in Oceanians.

Columns:
– chromosome, start, end, mean_posterior, length(bp), length(cM): see outputs from trace-summary (git repo “trace”)
– hmmix_start, hmmix_end, hmmix_overlap_length(bp), mean_pp, hmmix_assign: The start, end positions, overlapping length, mean posterior probability and archaic ancestry assignment for segments from hmmix results of the same haplotype that overlaps the current TRACE output archaic segment
– ibdmix_start, ibdmix_end, ibdmix_overlap_length(bp), ibdmix_max_length(bp), ibdmix_assign: The start, end positions, overlapping lengths, maximum length and archaic ancestry assignments for segments from IBDmix results of the same individual that overlaps the current TRACE output archaic segment
– dsnps: derived mutations (all NA in these tables to reduce file sizes)
– dsnps_marks: marks (ND00, ND01, ND10, ND11, other) for derived mutations
– DAF_YRI: derived allele frequency for mutations in YRI samples included in the ARG
– t1s: lower-end times of introgression branches in this segment
– t2s: upper-end times of introgression branches in this segment
– mutages: mutation ages for derived mutations
– branch_mark: marks for derived mutations showing if they are mapped (on, above, below) the introgression branch
– nderived, nderived_strict: number of derived alleles (that are in 1000 Genomes strict mask)
– ND00, ND10, ND01, ND11, ND00_strict, ND10_strict, ND01_strict, ND11_strict: number of (ND00, ND01, ND10, ND11) mutations on the segment (that are in 1000 Genomes strict mask)
– nd00_b, nd10_b, nd01_b, nd11_b, tot_b, yri_b: number of (ND00, ND01, ND10, ND11, total, shared with YRI) mutations mapped on the introgression branch
– nd00_prop, nd10_prop, n