Evidence map›Paper›PMID 28835989›Full record

ArticleJournal of molecular evolution2017

IDXL: Species Tree Inference Using Internode Distance and Excess Gene Leaf Count.

Sourya Bhattacharyya, Jayanta Mukherjee

Abstract read
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In one paragraph

Article in Journal of molecular evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
0.1field-weighted citation impact, top 49% of its field
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

0 citing papers in PubMed, 1 citations in OpenAlex.

No citing paper in PubMed yet.

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

2 authors at 1 institution in 1 country.

Sourya BhattacharyyaDepartment of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India. sourya.bhatta@gmail.com.ORCID 0000-0002-5767-8168
Jayanta MukherjeeDepartment of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India.
Indian Institute of Technology Kharagpur · IN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We propose an extension of the distance matrix methods NJst and ASTRID to infer species trees from incongruent gene trees having Incomplete Lineage Sorting. Both approaches consider the average internode distance (ID) between individual taxa pairs as the distance measure. The measure ID does not use the root of a tree, and thus may not always infer the relative position of a taxon with respect to the root. We define a novel distance measure excess gene leaf count (XL) between individual couplets. The XL measure is computed using the root of a tree. It is proved to be additive, and is shown to infer the relative order of divergence among individual couplets better. We propose a novel method IDXL which uses both the XL and ID measures for species tree construction. IDXL is shown to perform better than NJst and other distance matrix approaches for most of the biological and simulated datasets. Having the same computational complexity as NJst, IDXL can be applied for species tree inference on large-scale biological datasets.

Indexed as

AlgorithmsEvolution, MolecularGenesGenetic SpeciationAnimalsComputational BiologyMagnoliopsidaModels, GeneticPhylogenyVertebratesBootstrappingDeep coalescence (DC) or Incomplete Lineage Sorting (ILS)Excess gene leafGene tree/species tree incongruenceInternode distanceNeighbor Joining

Identifiers

PMID28835989
OpenAlexW2748812293

What OpenQuestion holds

Textmetadata
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Registered trials

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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.