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A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies
- N. Straube, Chenhong Li, Matthias Mertzen, Hao Yuan, T. Moritz
- BiologyBMC Evolutionary Biology
- 23 October 2018
BackgroundPrevious molecular studies on the phylogeny and classification of clupeocephalan fishes revealed numerous new taxonomic entities. For re-analysing these taxa, we perform target gene…
Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms
The results showed that the target gene tools yield data sets that provide robust inferences at a range of taxonomic scales in the Cyclophyllidea, consistent with the current consensus regarding cyclophyllides relationships.
Gene markers for exon capture and phylogenomics in ray‐finned fishes
A suite of “single‐copy” protein‐coding sequence (CDS) markers that may greatly enrich the batteries of exon markers for phylogenomic study in ray‐finned fishes are developed.
Assexon: Assembling Exon Using Gene Capture Data
- Hao Yuan, Calder J Atta, L. Tornabene, Chenhong Li
- BiologyEvolutionary bioinformatics online
- 1 September 2019
Assexon is a streamlined pipeline that de novo assembles targeted exons and their flanking sequences from raw reads and is a tool for accurate and efficient assembling of large read sets from exon capture experiments.
Exon-capture data and locus screening provide new insights into the phylogeny of flatfishes (Pleuronectoidei).
Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps
Inline-index method is a useful experimental design to clean up the data and address the contamination problem which has been plaguing high-throughput sequencing data in many applications.
Gene markers for exon capture and phylogenomics in ray-finned fishes
A suite of “single-copy” protein coding sequence (CDS) markers was identified through comparing eight fish genomes, and tested them empirically in 83 species (33 families and 11 orders) of ray-finned fishes, resulting in a selection of 4,434 markers which were proven to be useful in reconstructing phylogenies of the ray- Finned fishes at different taxonomic level.