ceqlogo [ -i <motif file> -m <id> | -i<id> <motif file> ]+ [options]


Load all motifs within a MEME motif file and write to logo.eps in EPS format:
ceqlogo -i meme.motifs -o logo.eps -f EPS

Load second motif from each of two files and shift the first one:
ceqlogo -i2 meme1.motifs -s 3 -i2 meme2.motifs -o logo.eps -f EPS


The ceqlogo program generates one or multiple, aligned logos in EPS or PNG format, based on a set of frequency matrices provided in the MEME file format. The code of ceqlogo is based on the Perl code of weblogo but is written in C and supports PNG output. Note that the program strives to use command line options similar to those of weblogo.

The letter stacks are calculated by the following equations found in Schneider and Stephens paper "Sequence Logos: A New Way to Display Consensus Sequences" and adapted from the weblogo documentation. The height of a letter is calculated as:

height(b,l) = f(b,l) * R(l)

where f(b,l) is the frequency of base or amino acid b at position l. The stack height R(l) is the amount of information present at position l and can be quantified as follows:

R(l) for amino acids = log(20) - (H(l) + e(n))

R(l) for nucleic acids = 2 - (H(l) + e(n))

where log is taken base 2, H(l) is the uncertainty at position l, and e(n) is the error correction factor for small sample sizes n. H(l) is computed as follows:

H(l) = - (Sum f(b,l) * log[ f(b,l) ])

where again, log is taken base 2. f(b,l) is the frequency of base b at position l. The sum is taken over all amino acids or bases.

The error correction factor e(n) is approximated by:

e(n) = (s-1) / (2 * ln 2 * n)


Motif File

A file containing one or more motifs in MEME format.


If no output file is specified ceqlogo writes to standard output.


Option Parameter Description Default Behavior
Options with arguments
-imotif file Load all motifs within the motif file.
-m id or num Load the numth motif or the motif whose ID is id within the motif file specified by the previous -i option.
-ix motif file Load the xth motif or the motif whose ID is x within the motif file.
-r Reverse-complement the logo for the previous -i or -m option.
-l Load motifs by IDs, preferentially. Load motifs in input order, preferentially.
-sshift Offset the previously loaded motif by shift.
-bbar bits Number of bits in bar (real # > 0). DNA motifs have a default height of 2 bits and protein motifs have a default height of 4.3 bits.
-ctic bits Number of bits between tic marks.
-eerror bar fraction Fraction of error bar to show (real # > 0).
-fEPS|PNG Set the format of the output. The output is created in EPS.
-F Create a frequency logo with stack height 1. Height of stack is information content of motif column.
-hlogo height Height of output logo in cm (real # > 0).
-oimage file Create an image called image file and send the output to it. Send the output to standard out.
-nsample number Set the sample count of the previously loaded motif to sample number. This value is used to calculate error bars. Use the sample count embedded in the motif file.
-ttitle label Set the title of the image to title label.
-wlogo width Width of output logo in cm (real # > 0)
-xx-axis label Label for x-axis.
-yy-axis label Label for y-axis.
-ppseudocount Pseudocount for motifs. A pseudocount value of 1 is used.
-dfineprint Print fineprint in small font at bottom of logo. "Ceqlogo
--testverbosity level Runs a self test, ignoring all other options. The verbosity level [0..3] is optional.
-S  Turn off small sample correction. Small sample correction is used.
-B  Toggle bar ends.
-E  Toggle error bar.
-O  Toggle outlining of characters.
-N  Toggle numbering of x-axis.
-X  Toggle boxing of characters.
-Y  Toggle y-axis.