ArticleBioinformatics (Oxford, England)2017
phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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.
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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.
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Who cites it
11 citing papers in PubMed.
- A unique symbiosome in an anaerobic single-celled eukaryote.Nature communications · 2024Article
- TADA: taxonomy-aware dataset aggregator.Bioinformatics (Oxford, England) · 2023Article
- Genome Comparison Reveals Inversions and Alternative Evolutionary History of Nutritional Endosymbionts in Planthoppers (Hemiptera: Fulgoromorpha).Genome biology and evolution · 2023Article
- Article
- Host Adaptation in Legionellales Is 1.9 Ga, Coincident with Eukaryogenesis.Molecular biology and evolution · 2022Article
- Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae).The ISME journal · 2022Article
- Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition.Nature communications · 2020Article
- miComplete: weighted quality evaluation of assembled microbial genomes.Bioinformatics (Oxford, England) · 2020Article
- Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT.Genome biology · 2019Article
- A Parasitic Arsenic Cycle That Shuttles Energy from Phytoplankton to Heterotrophic Bacterioplankton.mBio · 2019Article
- Resurrecting ancestral genes in bacteria to interpret ancient biosignatures.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2017Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Summary: With the wealth of available genome sequences, a difficult and tedious part of inferring phylogenomic trees is now to select genomes with an appropriate taxon density in the different parts of the tree. The package described here offers tools to easily select the most representative organisms, following a set of simple rules based on taxonomy and assembly quality, to retrieve the genomes from public databases (NCBI, JGI), to annotate them if necessary, to identify given markers in these, and to prepare files for multiple sequence alignment. Availability and Implementation: phyloSkeleton is a Perl module and is freely available under GPLv3 at https://bitbucket.org/lionelguy/phyloskeleton/ . Contact: lionel.guy@imbim.uu.se.
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Registered trials
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.