Work 112911 2124
2015-01-13azim58 - Work 112911 2124
Need to find an example glam2 command line call
glam2 directory:
C:\cygwin\home\Owner\meme\meme_4.6.1\src
C:\cygwin\home\Owner\meme\meme_4.6.1\src>glam2
FATAL: Usage: glam2 options alphabet my_seqs.fa
Main alphabets: p = proteins, n = nucleotides
Main options (default settings):
- h: show all options and their default settings
- o: output directory; will not clobber existing files
- O: output directory (glam2_out); allow clobbering
- r: number of alignment runs (10)
- n: end each run after this many iterations without improvement (10000)
- 2: examine both strands - forward and reverse complement
- z: minimum number of sequences in the alignment (2)
- a: minimum number of aligned columns (2)
- b: maximum number of aligned columns (50)
- w: initial number of aligned columns (20)
- Q: run quietly