glam2format [fasta|msf] <glam2 alignment>


This program reads in a motif found by glam2, and writes it in a standard alignment format (FASTA-with-gaps or MSF). This enables the alignment to be passed to third-party software, including graphical visualization tools such as Kalignvu, Boxshade, and WebLogo. On the other hand, not all the motif information is preserved: in particular, the key positions are lost. Only the top motif in glam2 output is converted.


Output Type

Choose to output sequences in FASTA-with-gaps or MSF.

GLAM2 Alignment

A GLAM2 motif.


The sequences are written to standard output unless -o is specified to send the output to a file.


Option Parameter Description Default Behavior
General Options
-ofile The sequences are written to file. The sequences are written to standard output.
-c Make a compact alignment.
-ffile Sequence file for flanking sequences

Usage Examples