KINN is a Novel Alignment-Free Method Based on the Inner Distance Distribution of Kmer Pairs,
The program is written in python (in Linux)
python kinn_main.py protein --seqs $inputsequences --medatacsv $sequences_labelname --k $k --savefolder $savefolder
python kinn_main.py -h
dna or protein (must input)
--seqs sequences file of species
--savefolder position of saving the distance
--k kmer(optional)
--medatacsv Species specific label (optional)
--metric distnace function, default='cosine'
--seqformat' default='fasta
Output is the mega style, you can directly pass it into mega X to obtain the phylogenetic tree.
python kinn_main.py protein --k 2 --seqs example.fasta --medatacsv example.csv --savefolder dis
Runbin Tang, Zuguo Yu, Jinyan Li, Inner distance distributions of k-mer pairs in biological sequences for alignment-free construction of accurate phylogeny trees