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Dollo Annotator App
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).
- DolloAnnotator requires Java at least version 8, which you can get here: https://adoptopenjdk.net/
- Download
DolloAnnotator.jar
from here: https://github.com/rbouckaert/Babel/releases/download/v0.3.0/DolloAnnotator.jar
- 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 downloadedDolloAnnotator.jar
- 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
, selectBabel
, clickInstall
).
- Start Dollo Annotator via the AppLauncher (Start BEAUti, select menu
File/Launch Apps
, selectDolloAnnotator
, clickLaunch
) - 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).
- 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
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;
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.
R Bouckaert, M Fischer, K Wicke. Combinatorial perspectives on Dollo-k characters in phylogenetics. under review 2020.