Constructs a phylogenetic tree in Newick tree format using .fasta or .paml nucleotide sequence files as input.
To compile using gcc under Linux (tested using version 7.3.1)
make AFP
g++ AFP.cpp -o AFP
./AFP filename.fasta
./AFP filename.paml
To generate a random phylogenetic tree with N nodes:
./AFP -random N
Running './AFP' without arguments or with a flag '-h' will display the help dialog with additional information.
To change the k-mer length used for constructing the distance matrix add flag -k N, e.g.:
./AFP filename.fasta -k 5
- Cosine distance (flag -c)
- Mahalanobis distance (flag -m)
- Fractional k-mer count (default)
The output of the functions will be stored in 'Newick_real.txt', 'Newick_synthetic.txt', or 'Newick_random.txt'.