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