rmes.composition  -seq DNA-sequence-file
                 [-phase] 
                 [-hmin <hmin>] [-hmax <hmax>]
                 [-eng[lish]]

-seq:

This option introduces the name of the input DNA sequence file.

-phase

When set, the phase (or reading frame) is taken into account.
The phase of a letter (base) in the sequence corresponds to its position in the sequence modulo 3. A given base can be in phase 1, 2 or 3. The phase of a given word in the sequence is defined to be the phase of its last letter in the sequence.

-hmin <hmin>, -hmax <hmax>

<hmin> introduces the minimal length of the words to be counted (by default, 1) and <hmax> the maximal length (by default <hmin>).

-eng[lish]

When set, the messages are in english.
By default, they are in french.

rmes.composition -seq lambda -phase -hmin 2 -eng

Title of the sequence :
LAMBDA     48502 bp ds-DNA    V00636 X00906 #

Length of the sequence : 48502

*** Phase 1 ***

aa : 1288 ag : 786 ac : 847 at : 1115 ga : 1149 gg : 984 gc : 1274 gt : 952
ca : 1111 cg : 1038 cc : 791 ct : 891 ta : 711 tg : 1221 tc : 892 tt : 1117


*** Phase 2 ***

aa : 1267 ag : 977 ac : 871 at : 1144 ga : 1030 gg : 1084 gc : 1082 gt : 833
ca : 1045 cg : 1072 cc : 872 ct : 815 ta : 699 tg : 1296 tc : 900 tt : 1180


*** Phase 3 ***

aa : 1138 ag : 969 ac : 856 at : 1078 ga : 1077 gg : 1111 gc : 1257 gt : 984
ca : 1058 cg : 1003 cc : 834 ct : 830 ta : 763 tg : 1276 tc : 884 tt : 1049


*** Without distinction of the phase *** 

aa : 3693 ag : 2732 ac : 2574 at : 3337 ga : 3256 gg : 3179 gc : 3613 gt : 2769
ca : 3214 cg : 3113 cc : 2497 ct : 2536 ta : 2173 tg : 3793 tc : 2676 tt : 3346

See the installation procedure of R'MES.