A comparison between the pipeline Captus and the pipeline it is supposed to replace, HybPiper.
Both pipelines align raw nucleotide sequence reads for the use of phylogenetic analyses.
I will use raw sequence reads from the tropical angiosperm genus Costus as a test dataset to compare their alignment processes and resulting phylogentic trees. Only a subset of the full data set will be used, specifically testinmg the placement of the new species C. flammulus.
As our ability to process high throughput data and the field of systematics grows, it is important to keep improving and testing the newest tools and pipelines available.
Captus Edgardo Mortiz
HybPiper Matt Johnson et al.
Full Costus dataset GenBank, Vargas et al.