Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines.

ABSTRACT:

Background

Despite recent advances, reliable tools to simultaneously handle different types of sequencing data (e.g., target capture, genome skimming) for phylogenomics are still scarce. Here, we evaluate the performance of the recently developed pipeline Captus in comparison with the well-known target capture pipelines HybPiper and SECAPR. As test data, we analyzed newly generated sequences for the genus Thladiantha (Cucurbitaceae) for which no well-resolved phylogeny estimate has been available so far, as well as simulated reads derived from the genome of Arabidopsis thaliana.

Results

Our pipeline comparisons are based on (1) the time needed for data assembly and locus extraction, (2) locus recovery per sample, (3) the number of informative sites in nucleotide alignments,

SUBMITTER: Raza M 

PROVIDER: S-EPMC10714463 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature