An implementation for the persistent phylogeny polynomial-time algorithm.
- gcc 5.0 and above
- Boost libraries
N.B. Skip this block if you already have Boost on your system
Popular Linux and Unix distributions such as Fedora, Debian, and NetBSD include pre-built Boost packages.
Debian example:
# apt install libboost-all-dev
Fedora:
Download Boost.
N.B. Skip this step if you already built Boost on your system
This implementation uses Boost.ProgramOptions to parse command line arguments and options, which means it needs
separately-compiled library binaries to work.
NB. Skip this step if you already updated your platform's environment variable
Moreover, on Unix systems, you may need to prepare plaform-specific settings (since Boost.ProgramOptions is a shared
library).
- Follow the steps at boost.org
$ git clone https://github.com/illoxian/persistent-philogeny.git
$ cd persistent-phylogeny
$ make
ppp [OPTION...] FILE...
ppp corresponds to the executable binary.
OPTION is a list of options - can be omitted.
FILE is a list of file paths (1 or more).
-h or --help
Display this message.
-v or --verbose
Display the operations performed by the program.
$ ./bin/ppp FILE...
The program will call the reduce function on each graph read from the files.
Examples:
Listing the single files
$ ./bin/ppp file1 dir1/file2 dir1/file3
Or with globs (if your shell supports it)
$ ./bin/ppp dir1/*
Or with options (order doesn't matter - still supports globs)
$ ./bin/ppp -m -v file1
The first line must contain the size of the matrix and the list of characters to be set as active. Empty lines (after
the first) are ignored.
Subsequent lines represent the matrix itself.
N M c0 c1 c2... ci...
Matrix made up of space-separated boolean values
Example which has no active characters by default:
6 3
0 0 1
0 1 0
0 1 1
1 0 0
1 0 1
1 1 0
Example which has the characters c0 and c2 active:
6 3 0 2
0 0 1
0 1 0
0 1 1
1 0 0
1 0 1
1 1 0