andriusbern / afp

Alignment-Free phylogenetic tree construction from .fasta sequence files

Alignment-Free phylogenetic tree construction

Constructs a phylogenetic tree in Newick tree format using .fasta or .paml nucleotide sequence files as input.

Instructions

Compiling

To compile using gcc under Linux (tested using version 7.3.1)

make AFP

g++ AFP.cpp -o AFP

Running with sequence files as input

./AFP filename.fasta

./AFP filename.paml

Generating random trees

To generate a random phylogenetic tree with N nodes:

./AFP -random N

Additional arguments

Running './AFP' without arguments or with a flag '-h' will display the help dialog with additional information.

k-mer length (default 8)

To change the k-mer length used for constructing the distance matrix add flag -k N, e.g.:

./AFP filename.fasta -k 5

Distance measures

1. Cosine distance (flag -c)
2. Mahalanobis distance (flag -m)
3. Fractional k-mer count (default)

Output

The output of the functions will be stored in 'Newick_real.txt', 'Newick_synthetic.txt', or 'Newick_random.txt'.