This package contains programs to help you prepare input files for PipMaker and analyze its output. The functionality of these two versions is virtually identical.
This program locates patterns of transcription factor binding sites within a MultiPipMaker text alignment file or a sequence file in FASTA format. It is written in C.
This package contains three programs for working with text alignment files from MultiPipMaker. Infocon identifies highly conserved regions using an information content approach. Multi_pat finds regions where every row matches a user-specified nucleotide pattern; for instance it can be used to find conserved patterns not represented by a weight matrix. Subalign extracts the aligned sequence of all species within one or more specified coordinate ranges. All are written in C.