Stitch or cluster? A comparison of alternative phylogenomic dataset assembly strategies for blenny fish

Phylogenomics has revolutionized the way we infer evolutionary relationships. Several bioinformatic pipelines have been developed for assembling phylogenomic datasets, in which orthology inference is a key step. Here, we compared two alternative strategies for assembling phylogenomic datasets: sequence clustering (OrthoFinder) and a new similarity-based approach that enriches a predefined set of loci (Patchwork). We downloaded publicly available genomic data for the fish family Blenniidae, which comprises a heterogeneous set of source data (genome skimming, transcriptomes, genomes) obtained by various sequencing technologies (Illumina short reads, long Nanopore reads, 454 pyrosequencing). These data are characterized by diverse levels of sequencing depth, read length, and per-base accuracy, representing a typical scenario of data reuse for phylogenomic purposes. All data types, regardless of accuracy and sequencing depth, were suitable to phylogenetically place species, even at estimate..., , # Data from: Stitch or cluster? A comparison of alternative phylogenomic dataset assembly strategies for blenny fish

Dataset DOI: [10.5061/dryad.gb5mkkx4g](https://doi.org/10.5061/dryad.gb5mkkx4g)

## Description of the data and file structure

This dataset contains the multiple sequence alignments and phylogenetic results of our study on the phylogeny of combtooth blennies (Blenniidae). We compared two alternative strategies for assembling phylogenomic datasets: sequence clustering (OrthoFinder) and a new similarity-based approach that enriches a predefined set of loci (Patchwork). We also explored two alternative approaches to combine marker-rich phylogenomic data with taxonomically broad multi-locus markers obtained by Sanger sequencing. 

## Files and variables

#### 1. Concordance_factors.zip

**concord.cf.branch:** gCF inferred by IQ-TREE on the Patchwork ASTRAL tree
**concord.cf.stat:** table of concordance factors inferred by IQ-TREE
**concord_v2_unresolved.cf.tree.tre:** Nexu..., ,