Skip to content

Commit

Permalink
updated documentation
Browse files Browse the repository at this point in the history
  • Loading branch information
qiyunzhu committed May 6, 2021
1 parent b1b6cb9 commit 42d63af
Show file tree
Hide file tree
Showing 2 changed files with 5 additions and 1 deletion.
4 changes: 4 additions & 0 deletions doc/classify.md
Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,10 @@ The difference from free-rank classification (2) is that, it discards all units

Multiple ranks can be specified simultaneously, delimited by comma (e.g., `--rank none,free,phylum,genus,species`), in which case Woltka will generate one [profile](output.md) for each rank. This is significantly faster than running Woltka multiple times on individual ranks.

### Default rank

One can omit the `--rank` parameter. In such case, Woltka automatically performs free-rank classification (2) (same as `--rank free`) if there is a classification system, or no classification (1) (same as `--rank none`) if there isn't.


## Ambiguous assignment

Expand Down
2 changes: 1 addition & 1 deletion doc/hierarchy.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ Woltka features a highly flexible hierarchical classification system. It is repr

The term "**rank**" (or "level") is still relevant, but it is merely a property of a feature, and does not bear information of hierarchy. For example, above a _genus_-level unit it does not have to be a _family_-level one, but could directly go to _order_, or have a _tribe_ which isn't common for the rest of the tree, or one or more nodes which do NOT have the rank assignment.

In another word, Woltka classification is **rank-free**. This design enables finer-grain resolution of feature relationships, in addition to flexibility. It is therefore suitable for complex systems, such as phylogenetic trees.
In another word, Woltka classification is **rank-independent**. This design enables finer-grain resolution of feature relationships, in addition to flexibility. It is therefore suitable for complex systems, such as phylogenetic trees.

That being said, Woltka still supports ranked hierarchies and one can instruct the program to target one or more specific ranks.

Expand Down

0 comments on commit 42d63af

Please sign in to comment.