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The binary representations of the DNA sequence data for phylogenetic analysis

The binary representations of the DNA sequence data for phylogenetic analysis

Evgeny V. Mavrodiev 59 Views
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In current molecular systematics the alignments of the DNA sequences are using for phylogenetic analysis without determination of character’ polarity. Also, modern molecular analyses require a priori knowledge of someone particular model(s) of the evolutionary process. For the first time, I re-coded matrices of the DNA characters as polarized binary matrices for future analyses. This makes molecular data informative as well as return scientist to the pure comparative thinking. As a result, the idea of the “evolutionary change” is involving to the research only a posteriori = as a general principle of explanation, not as part of the algorithm of the tree construction, as today.  Because no evolutionary model involved to the data analyses, my way of the handling molecular data is flexible and general. For example, from my standpoint, any evolutionary theory or even the aristotelean way of thinking seems to be semantically relevant to handle the DNA sequence data.

Impact

This idea has a broad impact. Due to the strict Hennigian background It may benefit the professional molecular systematists. My approach however is following the old discussions regarding the “pattern-cladism” (see this link for the brief and most recent review of the topic: https://peerj.com/articles/3578/) - perhaps one of the most influenced stream within Biology from the near past that impacted not only professional systematists but also philosophers, linguists, sociologist etc.

What I Will Do With $5,000

1. Any manipulations with the binary representations of the molecular data requires good computational resources. At the same time, many heavy analyses must be repeated again and again and thus the standard Online clusters are not appropriate for this kind of procedure, but the good personal desktop is necessary. Therefore I would like to use the part of 5000 USD to improve my recent home computer.

2. I need money to pay for the Open Access Publications. These are expensive at the moment.

Evgeny’s avatar

About Evgeny V. Mavrodiev

Dr. Evgeny V. Mavrodiev, Ph.D. Senior Biological Scientist & Lab. Manager Florida Museum of Natural History (FLMNH) University of Florida Main Campus Dickinson Hall, 301 Molecular Lab. of Plant Systematics PO Box 117800 Gainesville, FL 32611-7800 Phone: 352-273-1961 (work) 352-337-6697 (home) Fax: 352-846-2154 E-mail: evgeny@ufl.edu Publications (via Google Scholar): https://scholar.google.com/scholar?hl=en&q=Evgeny+Mavrodiev&btnG;=&as_sdt=1,10&as;_sdtp=

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