This is code used in a phylogenomic study of the ant subfamily Dorylinae. Please consider citing it if you are using the scripts:
Borowiec M. L. 2017. Convergent evolution of the army ant syndrome and congruence in big-data phylogenetics. bioRxiv.
Structure:
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├── aln_bin_by_rate.py # concatenate loci by rate into n bins
├── aln_choose.py # sample n loci across rate range
├── chronos_dating.R # Chronos divergence dating
├── compo_tests_corrected.py # compositional heterogeneity tests in p4
├── compo_tests_wrapper.py # wrapper for tests on multiple loci
├── compute_rcfv.py # compute RCFV (compositional heterogeneity)
├── print_upp_command.py # print UPP alignment commands
├── remove_misaligned.R # removing misaligned taxa from amino acid alignments
├── significance_tests.R # testing locus properties in matrices
├── tree_props.R # avg. bootstrap, branch length, saturation, plotting gene trees
└── upp_script.sh # UPP commands used for alignment of each locus