Evidence map›Paper›PMID 39628543›Full record

ArticleApplications in plant sciences

BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more.

Nelson R Salinas, Gil Eshel, Gloria M Coruzzi, Rob DeSalle, Michael Tessler, Damon P Little

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PubMed Full text at PMC Publisher
In one paragraph

Article in Applications in plant sciences. 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

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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

5 · Who and what money

Authors and funding

6 authors.

Nelson R SalinasLewis B. and Dorothy Cullman Program for Molecular Systematics The New York Botanical Garden, Bronx New York USA.ORCID 0000-0002-4812-8674
Gil EshelCenter for Genomics and Systems Biology New York University New York New York USA.
Gloria M CoruzziCenter for Genomics and Systems Biology New York University New York New York USA.
Rob DeSalleInstitute for Comparative Genomics American Museum of Natural History New York New York USA.
Michael TesslerLewis B. and Dorothy Cullman Program for Molecular Systematics The New York Botanical Garden, Bronx New York USA.
Damon P LittleLewis B. and Dorothy Cullman Program for Molecular Systematics The New York Botanical Garden, Bronx New York USA.ORCID 0000-0001-9635-6164

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Premise: Common steps in phylogenomic matrix production include biological sequence concatenation, morphological data concatenation, insertion/deletion (indel) coding, gene content (presence/absence) coding, removing uninformative characters for parsimony analysis, recording with reduced amino acid alphabets, and occupancy filtering. Existing software does not accomplish these tasks on a phylogenomic scale using a single program. Methods and Results: BAD2matrix is a Python script that performs the above-mentioned steps in phylogenomic matrix construction for DNA or amino acid sequences as well as morphological data. The script works in UNIX-like environments (e.g., LINUX, MacOS, Windows Subsystem for LINUX). Conclusions: BAD2matrix helps simplify phylogenomic pipelines and can be downloaded from https://github.com/dpl10/BAD2matrix/tree/master under a GNU General Public License v2.

Indexed as

concatenationgene contentgene presence/absenceindel codingmorphologyoccupancy filteringphylogenomicsreduced amino acid alphabets

Identifiers

PMID39628543
PMCPMC11610412

What OpenQuestion holds

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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.