GenerateTrees - Generate all or a random set of trees for a given set of taxon names
GenerateTrees is a commandline software that takes as input the number of unrooted binary trees you want generate and a file with the desired taxon names.
If the number given is 0, the program will generate all possible trees (can be many). Otherwise it draws randomly from the tree space with equal probability. Thus, trees can occur more than once in the output and the given number is allowed to be larger than the number of possible different trees.
If there is a third parameter given it is interpreted as the output filename, otherwise the generated trees will be written to stdout and can be piped (messages by the program are all written to stderr).
The file with the taxon names can either be an alignment in PHYLIP format (alignment length and sequences will be ignored) or just a text file, where the first line states the number of names which follow in the lines after.
GenerateTrees is written in C and is configured using the autotools. That means, running ./configure followed by make should typically do the job and produce an executable generatetrees in the folder src. This you may want to move to, e.g., your ~/bin or /usr/local/bin directory to make it generally accessible.
Further details can be found in the included README file.
If you use the program please cite the following: