Note: The SCF format (.scf) has been renamed to the SeqSel format (.seqsel) due to preexisting SCF formats that store data from DNA sequencing instruments. The .scf extension is still compatible with jevtrace.

The SeqSel sequence coloring format is designed to encode the coloring of individual sequences, multiple sequence alignments (MSA) and protein structures.

SeqSel is compatible with multiple types of alignments and structures, encoding universal features. The format is text based, human readable, and optimized for storage. Since the coloring data is valid only for a specific sequence or alignment, an optional checksum is added to each selection file to ensure consistency.


x1 x2 y1 y2 r g b

where (x1,y1) and (x2,y2) are alignment coordinates of the residue or alignment block


r,g,b are the Red Green and Blue RGB color channels.


A Sequence and Structure

Coloring Format

Download an example SeqSel file.

SeqSel was created by

Marcin Joachimiak

©UCSF, San Franscisco.

This page last updated 05/08/12

SeqSel has been published in Genome Biology along with jevtrace.

For an example of an application implemeting SeqSel. see Jevtrace. Jevtrace is a Java implementation of variations of the Evolutionary Trace method.

Example implementation screenshot

A description of the SeqSel format v2.1.


SeqSelis distributed under an open license allowing development and modification.

download the compressed SCFv2.1 Java package
View the SeqSel v2.1 Java source code.