edgeredef

finds repeat families from biological sequences

Install

All systems
curl cmd.cat/edgeredef.sh
Debian Debian
apt-get install repeatmasker-recon
Ubuntu
apt-get install repeatmasker-recon
image/svg+xml Kali Linux
apt-get install repeatmasker-recon
Windows (WSL2)
sudo apt-get update sudo apt-get install repeatmasker-recon
Raspbian
apt-get install repeatmasker-recon

repeatmasker-recon

finds repeat families from biological sequences

The RECON package implements a de novo algorithm for the indentification of repeat families from biological sequences. The program implements an approach for the de novo identification and classification of repeat sequence families that is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. The extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. When tested on the human genome, this approach was able to properly identify and group known transposable elements. The program, should be useful for first-pass automatic classification of repeats in newly sequenced genomes.