Scripts repository
_{for "Assessment of phylogenetic approaches to study the timing of recombination cessation on sex chromosomes"}

List of Contents

• Input/ folder
  • hypothetical_topologies/ folder
  • species_relative_time/ folder
• Script/ folder
  • BEAST_TN93_UCLD/ folder
  • run_BEAST_TN93/ folder
  • recsup_environment.yml
  • run_Codeml.sh
  • run_RAxML_ML_tree.sh
  • run_IQ-Tree_topology_test.sh
  • Approach_summary_plot.Rmd
  • Comparison_between_ELW_BEAST.Rmd
  • Species_combinations_BEAST.Rmd

Details

• hypothetical_topologies/ folder The folder contains the 12 hypothetical topologies in newick format. These hypothetical topologies are used in the ELW approach.

• species_relative_time/ folder The folder contains the relative time calibrations for dataset involving 1, 3, 6, 12 outgroups in the BEAST approach.

• BEAST_TN93_UCLD/ folder The folder contains bash script BEAST_TN93_UCLD_v.20210902.sh to generate BEAUTi configuration file and run BEAST2 on 1 alignment file. The template files, e.g., beast_template_12og.txt has most of the BEAUTi configuration file, including the priors of site model, clock model and tree model, and is used by BEAST_TN93_UCLD_v.20210902.sh to generate a complete BEAUTi configuration file.

• run_BEAST_TN93/ folder The folder contains bash scripts to run BEAST approach in parallel on a cluster computer. The scripts will use the files in BEAST_TN93_UCLD/ folder and species_relative_time/ folder.

• environment.yml This YAML file is used to setup the Conda environment for the analyses.

• run_Codeml.sh The bash script runs Codeml for the dS approach. The script is run locally.

• run_RAxML_ML_tree.sh The bash script constructs maximum likelihood tree using RAxML for the ML_CT approach. The script is run in parallel on a cluster computer.

• run_IQ-Tree_topology_test.sh The bash script runs topology test using IQ-Tree on a cluster computer. The script will use the files in hypothetical_topologies/ folder.

• Approach_summary_plot.Rmd The RMarkdown file has the codes to generate Fig. 3 and Fig. 5.

• Comparison_between_ELW_BEAST.Rmd The RMarkdown file has the codes to generate the major part of Fig. 4.

• Species_combinations_BEAST.Rmd The RMarkdown file has the codes to generate Fig. 6.

Appendix

To make it easy to code, the species abbreviation in the scripts are different from that in the paper. The translation can follow the table:

Species (Eng.)	Species (Latin)	Abbr. in the paper	Abbr. in the scripts
Great reed warbler	Acrocephalus arundinaceus	A. aru.	GRW
Clamorous reed warbler	Acrocephalus stentoreus	A. ste.	CRW
Marsh warbler	Acrocephalus palustris	A. pal.	MW
Western olivaceous warbler	Iduna opaca	I. opa.	IO
Savi’s warbler	Locustella luscinioides	L. lus.	LL
Bearded reedling	Panurus biarmicus	P. bia.	BR
Great tit	Parus major	P. maj.	GrT
Zebra finch	Taeniopygia guttata	T. gut.	ZeF
Blue-crowned manakin	Lepidothrix coronata	L. cor.	BlM
Budgerigar	Melopsittacus undulatus	M. und.	Bud
Chicken	Gallus gallus	G. gal.	Chi
Emu	Dromaius novaehollandiae	D. nov.	Emu
Green anole	Anolis carolinensis	A. car.	Ano