So far this github repository only contains a tool used in Springer et al. 2020 to convert a matrix of 0/1 characters (in PHYLIP or FASTA format) into a file of newick strings (one per line).

To compile and run the code, use the following commands:

cd phylotools/src
make
./run_binary_character_matrix_to_newick [input file] > [output file]

Note 1: You may need to edit the Makefile to replace G++ with your C++ compiler.

Note 2: If nothing is written to the output file, there may be having issues with the newline character used in your input file, as discussed here. To summarize, the input file must use \n as the newline character. If it was created on a Windows system, then \r\n may be used as the newline character. In this case, you can remove the \r characters from the input file with the following command:

tr -d '\r' < [input file] > [output file]

Similarly, if the file was created on an older Mac, the \r may be used as the newline character. In this case, you can replace all of the \r characters with the \n character using the following command:

tr '\r' '\n' < [input file] > [output file]