@@ -82,8 +82,8 @@ Launch _MSTclust_ without option to read the following documentation:
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@@ -82,8 +82,8 @@ Launch _MSTclust_ without option to read the following documentation:
* Specific rows can be selected using option `-r`.
* Specific rows can be selected using option `-r`.
* A [minimum spanning tree](https://en.wikipedia.org/wiki/Minimum_spanning_tree) and a [single-linkage hierarchical classification tree](https://en.wikipedia.org/wiki/Single-linkage_clustering) can be written in [GraphML](http://graphml.graphdrawing.org/index.html) and [Newick](http://evolution.genetics.washington.edu/phylip/newicktree.html) output files using options `-m` and `-h`, respectively. These two options require important running times when considering large datasets (e.g. > 5,000 rows).
* A [minimum spanning tree](https://en.wikipedia.org/wiki/Minimum_spanning_tree) and a [single-linkage hierarchical classification tree](https://en.wikipedia.org/wiki/Single-linkage_clustering) can be written in [GraphML](http://graphml.graphdrawing.org/index.html) and [Newick](http://evolution.genetics.washington.edu/phylip/newicktree.html) output files using options `-m` and `-h`, respectively. These two options require important running times when considering large datasets (e.g. > 5,000 rows).
* By definition, setting small cutoff values yield clustering with a large number of classes with fast running times.
* By definition, setting small cutoff values yield clustering with a large number of classes with fast running times.
* Profile length is required to carry out data perturbation analyses (option `-L`).
* Profile length is required to carry out data perturbation analyses (option `-L`). For each statistics, _MSTclust_ will compute the average value and the 95% CI based on different replicates (option `-R`).
* Data subsampling analyses progressively subsample raw data with rate values _b_/(_B_+1) where _b_ = 1 ... _B_ and _B_ > 1 is the number of bins specified using option `-B`. At least _B_ = 9 bins (i.e. rates = 10%, 20% ... 90%) are recommended.
* Data subsampling analyses progressively subsample raw data with rate values _b_/(_B_+1) where _b_ = 1 ... _B_ and _B_ > 1 is the number of bins specified using option `-B`. At least _B_ = 9 bins (i.e. rates = 10%, 20% ... 90%) are recommended. For each statistics, _MSTclust_ will compute the average value and the 95% CI based on different replicates (option `-R`).
* For more details on the profile distance computation, clustering algorithm and descriptive statistics, see the technical notes pdf file.
* For more details on the profile distance computation, clustering algorithm and descriptive statistics, see the technical notes pdf file.
