ctl43/TiMEstamp: TiMEstamp v0.1.0 — Initial public release

TiMEstamp (Timing Mobile Element Insertions from Multiple Sequence Alignments) is an R package for estimating the evolutionary insertion timepoints of mobile elements using multiple sequence alignments (MSAs) of genome assemblies. This initial release provides all core functionalities for converting, analyzing, and interpreting transposable element insertions.

Key features

• MAF-to-FASTA conversion: Convert per-chromosome MAF alignment blocks into per-species FASTA files aligned to a reference genome.
• Gap extraction: Identify unaligned regions (gaps) relative to the reference and export them as BED or GRanges objects.
• Insertion timepoint estimation: Infer evolutionary insertion timing based on coverage across sister clades.
• Chimera prediction: Detect candidate chimeric insertions formed at the 5′ end of LINE-1 elements.

Citation If you use TiMEstamp in your research, please cite: Law CT, Burns KH. Comparative Genomics Reveals LINE-1 Recombination with Diverse RNAs. bioRxiv [Preprint]. 2025 Feb 3. doi:10.1101/2025.02.02.635956 Or the latest publication linked to this preprint.

Repository GitHub: https://github.com/ctl43/TiMEstamp