Evidence map›Paper›PMID 30314446›Full record

ArticleBMC bioinformatics2018

PQ, a new program for phylogeny reconstruction.

Dmitry Penzar, Mikhail Krivozubov, Sergey Spirin

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Dmitry PenzarFaculty of Bioengineering and Bioinformatics, Moscow State University, 1 Leninskiye Gory, bld. 73, Moscow, 119991, Russia.
Mikhail KrivozubovGamaleya Center of Epidemiology and Microbiology, 18 Gamaleya st., Moscow, 123098, Russia.
Sergey SpirinFaculty of Bioengineering and Bioinformatics, Moscow State University, 1 Leninskiye Gory, bld. 73, Moscow, 119991, Russia. sas@belozersky.msu.ru.ORCID http://orcid.org/0000-0002-8041-1808

Funding

Russian Science Foundation 16-14-10319
6 · The paper itself

Abstract

backgroundMany algorithms and programs are available for phylogenetic reconstruction of families of proteins. Methods used widely at present use either a number of distance-based principles or character-based principles of maximum parsimony or maximum likelihood.

resultsWe developed a novel program, named PQ, for reconstructing protein and nucleic acid phylogenies following a new character-based principle. Being tested on natural sequences PQ improves upon the results of maximum parsimony and maximum likelihood. Working with alignments of 10 and 15 sequences, it also outperforms the FastME program, which is based on one of the distance-based principles. Among all tested programs PQ is proved to be the least susceptible to long branch attraction. FastME outperforms PQ when processing alignments of 45 sequences, however. We confirm a recent result that on natural sequences FastME outperforms maximum parsimony and maximum likelihood. At the same time, both PQ and FastME are inferior to maximum parsimony and maximum likelihood on simulated sequences. PQ is open source and available to the public via an online interface.

conclusionsThe software we developed offers an open-source alternative for phylogenetic reconstruction for relatively small sets of proteins and nucleic acids, with up to a few tens of sequences.

Indexed as

PhylogenyAlgorithmsSoftwareAlgorithmOpen source softwarePhylogeny reconstructionProtein evolutionWeb interface

Identifiers

PMID30314446
PMCPMC6186109

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.