Transposable element subfamily annotation has a reproducibility problem

The role of gene conversion between Transposable Elements in rewiring regulatory networks

(2019) Jeffrey A Fawcett et al.   Genome Biology and Evolution

Frequent nonallelic gene conversion on the human lineage and its effect on the divergence of gene duplicates

(2017) Arbel Harpak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Inference of Transposable Element Ancestry

(2014) Aaron C. Wacholder et al.   PLoS Genetics

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

The Rate and Tract Length of Gene Conversion between Duplicated Genes

(2011) Sayaka P. Mansai et al.   Genes

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS