This repository contains the data related to the publication:
Ludovic Dutoit,† Kieren J. Mitchell†, Nicolas Dussex, †, Catherine M. Kemper, Petter Larsson, Love Dalén, Nicolas J. Rawlence and , Felix G. Marx. Convergent evolution of skim feeding in baleen whales.
It is meant to ensure reproducibility and trace analyses in the paper. Please get in touch with nicolas.dussex@gmail.com and/or ludovic.dutoit@otago.ac.nz for any questions.
The bcftools_consensus_genome.bsh script uses a bcf file and an assembly to build a new consensus genome
This is recorded SNPCalling_clean.md that includes masking and splitting all the way to one file per window with all species.
Saved as one file in build_trees_clean.md that includes the astral analysis. Astral visualisations are not included, but scripts are availabe upon request.
The bcftools_consensus_genome.bsh is used to split a bam file into diplois.fastq file which is then used as input in the Pygmy_whale_PSMC_bootstrap.bsh to run the PSMC.