Ficus-RAD

Genomics workflow for RAD-seq analysis of Ficus

Reproducible code

Assembly and analysis of the data is documented in Jupyter-notebooks. To reproduce our results start by assembling the data by running the first notebook, followed by executing each analysis notebook which uses the assembled data sets created in the first notebook.

Assembly

• NB1: Assemble RAD-seq libraries with ipyrad

Analysis

• NB2: Phylogeny: ML analysis with RAxML

• NB3: Phylogeny: Species-tree analysis with tetrad

• NB4: Phylogeny: Species-tree analysis with BPP

• NB5: Admixture: STRUCTURE analysis

• NB6: Admixture: ABBA-BABA analysis

Links to figures outside of notebooks

• Shared RAD-seq data in c85d5f2_min4_s3k

• Tree+structure pharma

• Tree+Structure Americana