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README.md

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+---
+license: mit
+tags:
+  - dna
+  - genomics
+  - tokenization
+---
+
+# EvoLen — token analysis input data
+
+Derived interval files needed to reproduce the token analyses in Section 4 of
+*EvoLen: Evolution-Guided Tokenization for DNA Language Model*
+([arXiv:2604.08698](https://arxiv.org/abs/2604.08698)).
+
+Analysis code lives in the [`evolen` repository](https://github.com/mtapia-pacheco/evolen)
+under `analysis/`.
+
+## Contents
+
+```text
+region_beds/
+  conservation_crossed/    regions crossed with conservation category
+                           {promoter,enhancer,exon,intron}_{conserved,neutral,accelerated}.bed
+                           conservation_{conserved,neutral,accelerated}.bed
+  simple/                  the same four regions without the conservation split
+ccre_classes/              ENCODE SCREEN cCRE classes as BED, one file per class
+                           CA, CA-CTCF, CA-H3K4me3, CA-TF, PLS, TF, dELS, pELS
+                           *_balanced.bed are downsampled to the smallest class (26,102)
+motifs/motifs.txt          JASPAR 2024 vertebrate motifs, thresholded to consensus
+                           sequences (PWM positions at 0.5, wildcards trimmed, <= 12 bp)
+```
+
+`region_beds/conservation_crossed/` backs the P4 enrichment analysis (Figure 3);
+`ccre_classes/` backs the Multi-SCREEN task construction; `motifs/` backs the P1 motif
+preservation analysis (Figure 2A).
+
+## Not included — fetch these yourself
+
+Two inputs are public reference data and are not mirrored here.
+
+**hg38 reference genome** (~3.3 GB):
+
+```bash
+wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
+gunzip hg38.fa.gz && samtools faidx hg38.fa
+```
+
+**phyloP conservation scores.** The analysis reads per-chromosome bedGraph, which is a
+mechanical conversion of the public bigWig (~70 GB expanded, so it is regenerated rather
+than distributed):
+
+```bash
+wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP100way/hg38.phyloP100way.bw
+# convert per chromosome with UCSC bigWigToBedGraph
+bigWigToBedGraph -chrom=chr1 hg38.phyloP100way.bw chr1.bedGraph
+```
+
+Point `process_bedgraph_all.py --bedgraph_dir` at the directory of resulting
+`.bedGraph` files to produce the `{chrom}_phylop_segment.csv` files that drive both
+tokenizer construction and the phyloP analyses.
+
+## Usage
+
+```bash
+export EVOLEN_ROOT=/path/to/your/data_root     # analysis scripts resolve paths from this
+```
+
+Related: [token_evaluation](https://huggingface.co/datasets/nancyH/token_evaluation)
+hosts the phyloP analysis *outputs* (per-token aggregates used for Figure 2C).