Skip to content

Dollo Annotator App

Jump to bottom Edit New page
Remco Bouckaert edited this page Nov 23, 2020 · 2 revisions

Dollo Annotator is an application that can annotate tree with k-Dollo information and calculate Dollo-k characters (i.e. count the number of Dollo-k patterns).

There are two version that do exactly the same: a standalone app (recommended if you do not already have BEAST 2 installed), and a BEAST 2 app (recommended if you already have BEAST 2 installed).

Standalone App installation and starting

Installation

Starting

  • Start Dollo Annotator by double clicking the DolloAnnotator.jar in a file browser.
  • Alternatively, from a terminal, you can start it using java -jar /path/to/DolloAnnotator.jar where /path/to the path to where you downloaded DolloAnnotator.jar

BEAST App installation and starting

Installation

  • Install BEAST 2 for your operating system, available via http://beast2.org
  • Install Babel package v0.4.0 or better via the package manager (Start BEAUti, select menu File/Manage Packages, select Babel, click Install).

Starting

  • Start Dollo Annotator via the AppLauncher (Start BEAUti, select menu File/Launch Apps, select DolloAnnotator, click Launch)
  • Alternatively, from a terminal, you can start it using /path/to/beastbin/applauncher DolloAnnotator where /path/to/beastbin/ the path to where startup scripts for BEAST applications are (BEAST\bat\ in Windows, /beast/bin/ in OS X and Linux).

Dollo Annotator Options

  • tree: file containing a tree(s) of interest
  • nexus [filename]: nexus file with binary alignment used to annotate tree. If not specified, the tree is not annotated
  • out [filename]: file to write annotated tree into, or stdout if not specified (default: none)
  • filter [string]: specifies which subset (if any) of the sites in the input alignment should be selected. First site is 1.Filter specs are comma separated, either a singleton, a range [from]-[to] or iteration [from]:[to]:[step]; 1-100 defines a range, 1-100 or 1:100:3 defines every third in range 1-100, 1::3,2::3 removes every third site. Default for range [1]-[last site], default for iterator [1]:[last site]:[1]
  • range [string]: range for which to calculate the Dollo-k counts. Either a single number k to calculate the Dollo-k value, or a lower and upper bound (inclusive) separated by a comma for a range. If not specified, all values are calculated.
  • verbose [true|false]: display extra information, like progress of Dollo counting (default: false)
  • help show arguments

From a terminal, these options are accessible as command line arguments. For example

java -jar /path/to/DolloAnnotator.jar -tree input.trees -out Dollo-k.dat -range 1,5

to write Dollo-k counts for the range k=1 to 5 into file Dollo-k.dat for all trees in the file input.trees

File formats

The tree file can be in NEXUS or Newick format, for example for two trees with like so:

((((a,b),c),d),e);
((((a,b),c),d),e);

The NEXUS file with and alignment should contain binary sequences only. For example for a tree with five taxa this could be like so:

#NEXUS
begin characters;
        dimensions nchar=32 ntax=5;
        format datatype=binary symbols = "01";
        matrix
a 0000 0000 0000 0000 1111 1111 1111 1111 
b 0000 0000 1111 1111 0000 0000 1111 1111 
c 0000 1111 0000 1111 0000 1111 0000 1111 
d 0011 0011 0011 0011 0011 0011 0011 0011 
e 0101 0101 0101 0101 0101 0101 0101 0101 
;
end;

Post processing

When annotating a tree, the tree can be visualised with FigTree. To see the reconstruction, select "Branch Label" and choose "dollo" in the drop down box for items that can be displayed.

Citation

R Bouckaert, M Fischer, K Wicke. Combinatorial perspectives on Dollo-k characters in phylogenetics. under review 2020.

Add a custom footer
Add a custom sidebar
Clone this wiki locally