Script for annotating a BEAST .trees file (such as a maximum clade credibility tree from TreeAnnotator) so that it is better formatted for visualization by FigTree.
To run this script, create an input file with the format described below. Then run this script by typing the script name followed by the name of the input file:
mutpath_annotate_tree.py infile.txt
Or if the script is not executable on your platform:
python mutpath_annotate_tree.py infile.txt
TreeAnnotator can be used to create a .trees file that can be visualized with FigTree. However, the visualization will typically not look very good. Although it can be manually edited within FigTree, this script automates some of the annotations. Specfically, it allows you to show a set of user-specified names for just a subset of the branch tips. It also orders the tree nodes in ascending order.
Below is an example input file. After running the script on this input file, the new outtreefile file will be better formatted for opening by FigTree. Specifically, tip node names will only be shown for tips listed in the input file.
The input file is a text file. Empty lines or lines beginning with # are ignored. Otherwise, the first line should have the key intreefile and then give the .trees file that we are annotated. The next line should have the key outtreefile and then give the name of the new output .trees file with the annotations. If outtreefile already exists, it is overwritten. Remaining lines should then give tip names as they are specified in intreefile followed by a space and the name that is given to that tip in the annotated tree. If a tip name is not listed, it is not annotated in the tree. Typically, if you are working with a large tree then you may want to annotate only a small subset of the tips. Here is an example input file:
# input file for mutpath_annotate_tree.py
intreefile prot_maxcladecredibility.trees
outtreefile annotated_maxcladecredibility.trees
A/Aichi/2/1968_1968.50 Aichi/1968
A/Brisbane/10/2007_2007.10 Brisbane/2007
After running the script on this input file, two tips will be annotated as Aichi/1968 and Brisbane/2007, and the others will not be annotated.