0.2

README.md

@@ -48,28 +48,31 @@ Launch _MSTclust_ without option to read the following documentation:
 
  OPTIONS:
 
- -i <infile>    input file containing  either tab-delimited  profiles or a
+ -i <infile>    input file  containing  either tab-delimited  profiles or a
                 lower-triangular distance matrix (mandatory)
  -o <basenmae>  basename for output files (mandatory)
  -r <string>    selecting only specified rows (default: "1-")
- -l <string>    (input tab-delimited profiles) field(s) containing profile
+ -l <string>    (input tab-delimited profiles)  field(s) containing profile
                 labels (default: "1")
- -p <string>    (input tab-delimited profiles)  fields containing profiles
+ -p <string>    (input tab-delimited profiles)  fields  containing profiles
                 (default: "2-")
- -e <float>     (input tab-delimited profiles)  maximum allowed proportion
+ -e <float>     (input tab-delimited profiles)  maximum allowed  proportion
                 of empty entries per profile (default: 0.25)
  -c <float>     inclusive cutoff to define cluster(s) (default: not set)
- -S <integer>   seed value for data perturbation  and subsampling analyses
+ -g <integer>   generalized  mean   exponent   for  computing  silhouettes;
+                negative or positive infinity can be set using -inf or inf,
+                respectively (default: 1  i.e. arithmetic mean)
+ -S <integer>   seed value for  data perturbation  and subsampling analyses
                 (default: 0)
- -L <integer>   profile length  to carry  out data  perturbation  analysis
+ -L <integer>   profile length  to  carry out  data  perturbation  analysis
                 (default: not set)
- -B <integer>   number of  bins to  carry out  data  subsampling  analyses
+ -B <integer>   number  of  bins to  carry out  data  subsampling  analyses
                 (default: not set)
- -R <integer>   number of replicates for data perturbation and subsampling
+ -R <integer>   number of replicates for  data perturbation and subsampling
                 analyses (default: 100)
- -h             writing a single-linkage  hierarchical classification tree
+ -h             writing a  single-linkage  hierarchical classification tree
                 into an output file (default: not set)
- -m             writing  a  minimum  spanning  tree  into an  output  file
+ -m             writing  a  minimum  spanning  tree  into  an  output  file
                 (default: not set)
 ```