This source is an extension of Adam Rambaut's FigTree. The original source can be found here: https://github.com/rambaut/figtree/releases

Command line FigTree summary

Build Requirements (for further modifying the source code): java 8

Execution: A current version of figtree.jar can be found in dist/figtree.jar

Example execution:

Start the FigTree application and display the FigTree application frame to use in typical manual mode java -jar figtree.jar

To use as part of a pipeline (or run command line):

Easiest way to execute multiple files in a directory (For this example a folder named "1_TEST4_GP_DIVEIN_results"):

1. For easiest, default execution, all .tre files expected to be run should be named something like: TEST4_2315_160-161-170_GP_phyml_tree.txt

   • the important part of the file naming is that time points are parseable from the file name programmatically using the hyphens. In this case the software will try to pattern match and color based on the names containing: TEST4_2315_160 TEST4_2315_161 TEST4_2315_170

     note: hyphens not delineating time points should be avoided in the file names

   • coloring will occur automatically for each time point found

Single file execution:

Replace {AVG_LENGTH} with the average sequence length (e.g. 2500) Replace {PATH_TO_FILE} with the path to the newick tree file (DiveIn / PhyML output file e.g. TEST4_2315_160-161-170_GP_phyml_tree.txt)

java -jar figtree.jar -avg_seq_length {AVG_LENGTH} -colors extract -newickexport -nexusexport -graphic SVG -height 768 -width 783 {PATH_TO_FILE}

Batch execution of files in a folder using the same settings file:

find ./RESULTS_FOLDER_NAME/ -name '*phyml_tree.txt' -type f | awk '{print "java -jar figtree.jar -avg_seq_length {AVG_LENGTH} -colors extract -newickexport -nexusexport -graphic SVG -height 768 -width 783 "$0}' |sh

^ This command finds all files that include '*phyml_tree.txt' in their name, then prepends "java -jar figtree.jar -settings GP.settings -colors extract -newickexport -nexusexport -graphic SVG -height 768 -width 783 " to the path to each file that is listed. The "|sh" on the end of the command causes the execution of each line. If you run the command without the "|sh" you can see the lines that are built without executing them.

Command line parameters:

java -jar figtree.jar

-avg_seq_length (replace with the average length of sequence)
-colors extract (Using the keyword "extract" will attempt to find any values seperated by a "-" and append them to the prefix of the file name. Alternatively a comma delimited list of KEY:VALUE pairs (KEY is text to match with a hex color VALUE - e.g. V704_0026_232:#3333ff,V704_0026_231:#ff3300)
-newickexport (flag to include an exported ordered Newick formatted tree with the same name as graphic file)
-nexusexport (flag to include an exported ordered Nexus formatted tree with the same name as graphic file)
-graphic FORMAT as either (SVG, PDF, PNG, JPEG) 
-height HEIGHT (generally ignored when run from the command line. height will get automatically set)
-width WIDTH (default is 768, which works well when displaying in Phylobook)

Alternative example execution with manual color pattern match settings and output file naming:

Using the example above, TEST4_2315_160-161-170_GP_phyml_tree.txt, we can set the colors for the time points in a string for the -colors option:

e.g. -colors TEST4_2315_160:#3333ff,TEST4_2315_161:#ff33ff,TEST4_2315_170:##66ff66

To execute:

java -jar figtree.jar -avg_seq_length 2500 -colors TEST4_2315_160:#3333ff,TEST4_2315_161:#ff33ff,TEST4_2315_170:##66ff66 -newickexport -nexusexport -graphic SVG -height 768 -width 783 TEST4_2315_160-161-170_GP_phyml_tree.txt