I have NCBI GenBank mined DNA sequences belonging to matK and ITS2 regions. I would appreciate if anyone suggests alignment free tools to calculate K-mer frequencies OR Genetic distances in order to use them for phylogeny construction OR for classifying using machine learning classifiers (I use WEKA... any suggestions?).
Sorry I don't know if it will help you, although i send u.
matK-QR classifier: a patterns based approach for plant species identification
Ravi Prabhakar More, Rupali Chandrashekhar Mane, and Hemant J. Purohit
Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals
Hui Yao, Jingyuan Song, [...], and Shilin Chen
Sorry I don't know if it will help you, although i send u.
matK-QR classifier: a patterns based approach for plant species identification
Ravi Prabhakar More, Rupali Chandrashekhar Mane, and Hemant J. Purohit
Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals
Hui Yao, Jingyuan Song, [...], and Shilin Chen
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-S14-S9
Efficient alignment-free DNA barcode analytics
See the above article
A. K. M. Sharoar Jahan Choyon, thank you for your response. The matK-QR classifier generates matK gene specific signatures as QR codes and does not seems to be an algorithm that exhibits species discrimination potential based on any character or distance based method.
Ruhin Chowdhury thank you for suggesting this wonderful article, I have referred it already. Moreover, do you have any experience on using those tools, if yes kindly share your views on multi-class classifiers.
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