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PQ, a new program for phylogeny reconstruction.

Dmitry Penzar¹, Mikhail Krivozubov², Sergey Spirin^3,4,5

¹Faculty of Bioengineering and Bioinformatics, Moscow State University, 1 Leninskiye Gory, bld. 73, Moscow, 119991, Russia.

BMC Bioinformatics

|October 14, 2018

Summary

A new phylogenetic reconstruction program, PQ, offers an open-source alternative for analyzing protein and nucleic acid sequences. PQ shows improved accuracy over existing methods for smaller datasets and is less prone to long branch attraction.

Keywords:

Algorithm Open source software Phylogeny reconstruction Protein evolution Web interface

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Area of Science:

Bioinformatics
Computational Biology
Evolutionary Biology

Background:

Phylogenetic reconstruction is crucial for understanding evolutionary relationships.
Current methods rely on distance-based or character-based principles like maximum parsimony and maximum likelihood.

Purpose of the Study:

To develop a novel, open-source program for phylogenetic reconstruction.
To evaluate the performance of the new program against existing methods.

Main Methods:

Developed a new character-based algorithm implemented in the PQ program.
Tested PQ on natural and simulated sequence alignments.
Compared PQ's performance against maximum parsimony, maximum likelihood, and FastME.

Main Results:

PQ improves phylogenetic reconstruction accuracy for natural sequences compared to maximum parsimony and maximum likelihood.
PQ outperforms FastME on small sequence alignments (10-15 sequences) and is less susceptible to long branch attraction.
FastME outperforms PQ on larger alignments (45 sequences) and is superior to maximum parsimony/likelihood on natural sequences.
Both PQ and FastME are outperformed by maximum parsimony and maximum likelihood on simulated sequences.

Conclusions:

PQ provides an open-source alternative for phylogenetic reconstruction of small protein and nucleic acid datasets.
The program is accessible via an online interface.