ArticleEvolutionary bioinformatics online2018
HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees.
Article in Evolutionary bioinformatics online, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 69 citations in OpenAlex.
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- New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq).Frontiers in plant science · 2022Article
- Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae).Systematic biology · 2021Article
- New targets acquired: Improving locus recovery from the Angiosperms353 probe set.Applications in plant sciences · 2021Article
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- An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae.Applications in plant sciences · 2019Article
- HybSuite: An integrated pipeline for hybrid capture phylogenomics from reads to trees.Applications in plant sciencesArticle
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryHybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecies coalescent-based species tree reconstruction. HybPhyloMaker is written in BASH and integrates common bioinformatics tools. It can be launched both locally and on a high-performance computer cluster. Compared with existing target enrichment data analysis pipelines, HybPhyloMaker offers the following main advantages: implementation of all steps of data analysis from raw reads to species tree reconstruction, calculation and summary of alignment and gene tree properties that assist the user in the selection of "quality-filtered" genes, implementation of several species tree reconstruction methods, and analysis of the coding regions of organellar genomes. AVAILABILITY: The HybPhyloMaker scripts, manual as well as a test data set, are available in https://github.com/tomas-fer/HybPhyloMaker/. HybPhyloMaker is licensed under open-source license GPL v.3 allowing further modifications.
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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.