SYNOPSIS

repeatmasker-recon seq_name_list_file MSP_file integer

DESCRIPTION

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.

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.