Code from the publication: Johnson, O., Howard, J. T., and Brumfield, R. T. 2020. Systematics of a Neotropical clade of dead-leaf-foraging antwrens (Aves: Thamnophilidae; Epinecrophylla). Molecular Phylogenetics and Evolution 154:106962
Published paper: https://doi.org/10.1016/j.ympev.2020.106962
Data repository: https://doi.org/10.5061/dryad.r2280gb9n
Many of these scripts use tools from the Phyluce package: https://phyluce.readthedocs.io/en/latest/
Included scripts:
barcode_checks_co1.sh: check mitochondrial by catch against CO1 barcodes for contamination
Epinecrophylla_2500_phyluce.pbs: process and align UCE contigs with Phyluce, estimate RAxML phylogeny
Epinecrophylla_iqtree.pbs: Estimate UCE phylogeny with IQ-TREE
Epinecrophylla_mtDNA_tree.pbs: Estimate mitochondrial phylogeny with RAxML
Epinecrophylla_seqcap_pop_pipeline_NoOutgroup_reduced_to_clade.sh: Phase samples with seqcap_pop (https://github.com/mgharvey/seqcap_pop)
Epinecrophylla_vcftools_reduced_toClade_noOutgroup.sh: Process and filter seqcap_pop output with vcftools
exabayes.submit: Estimate UCE phylogeny with ExaBayes
format_and_plot_STRUCTURE_results.sh: Format and plot STRUCTURE results
gene_trees-all_UCEs-Epinecrophylla.sh: Estimate UCE gene trees with RAxML
jmodeltest_STACEY.sh: Calculate UCE partition schemes with jmodeltest
MITObim_epinecrophylla.sh: Harvest mitochondrial bycatch from with MITObim
plot_histogram.R: Plot histograms of intra- and inter-specific genetic distance matrices
prune_tips_for_SNAPP.R: Prune tree tips for SNAPP
reroot_tree.R: Re-root tree for input into treePL
Robinson-Foulds_distance.R: Calculate RF distance between trees
run_illumiprocessor.sh: Run illumiprocessor
sed_replace_str_sample_names_individually.sh: replace tree tip names with sed
SNAPP_runs_with_priors_run1.sh: Run SNAPP
structure_Epinecrophylla_pyrrhonota.sh: Run STRUCTURE
trim_cleaned_reads.sh: subsample cleaned UCE reads
trim_raw_reads.sh: subsample raw UCE reads