Scripts and templates to accompany "Dollo parsimony overestimates ancestral gene content reconstructions"

• AfterPhylo.pl: Manipulate trees after phylogenetic reconstruction.

• Orthofinder_orthogroups_to_probabilities.pl: Parse OrthoFinder (https://github.com/davidemms/OrthoFinder) orthogroups, sequence IDs and a directory of BLAST/DIAMOND results to produce presence probabilities for each species in each cluster using the empirical cumulative E value distribution.

• PASTA_probabilities_to_binary.pl: Convert probabilities in a PASTA file to binary values (all non-zero values are changed to 1).

• add_counter_to_tree.pl: Read a tree file, looking for characters matching "__". Replace each instance with a counter, starting from zero.

• add_underscores_to_internal_nodes_paste_tree.pl: Read tree file, replace internal node names with "__".

• batch_interproscan.pl: Run InterProScan to search Pfam domains in a directory of FASTA files.

• combine_simulation_output.pl: Go through a directory of Dollop or Bppancestor (https://github.com/BioPP) results for different simulations and produce one output file summarizing results for all simulations.

• create_bpp_config_files.pl: For each file in the input directory, modify the template to replace the string placeholder with the name of the file, and save the modified template to the output directory.

• dollop_state_at_node.pl: Parse the output of Dollop from the PHYLIP package (https://phylipweb.github.io/phylip/) to count the number of genes at each inferred ancestral node.

• interproscan_to_binary_PASTA.pl: Go through a directory of InterProScan (https://www.ebi.ac.uk/interpro/) results (ending in .tsv) and group together domains, outputting a binary PASTA format.

• move_and_rename_batch_dollop.pl: Copy PHYLIP Dollop output files from a set of input directories to a single output directory.

• parse_bppancestor_probabilities.pl: Read input of Bppancestor and summarize the number of ancestral genes present at each node.

• remove_internal_node_names.pl: Read a tree file and remove internal node names.

• rename_PASTA_headers.pl: Rename the headers of a PASTA file.

• resolve_multifurcations_in_tree.R: Transform all polytomies into a series of dichotomies.

• bash_dollop: Create a directory for each input file inside the current directory and run PHYLIP Dollop with an input tree and printing states at all nodes of the tree.

• bppancestor_input_simulations.zip: Simulated dataset input data files for Bppancestor.

• dollop_input_simulations.zip: Simulated dataset input data files for PHYLIP Dollop.

• named_eukprot_binaries.zip: Pfam domain content reconstruction input data files for Bppancestor.

• dollop_input.phylip: Pfam domain content reconstruction input data files for PHYLIP Dollop.

• template_bppancestor_config_file.conf: Configuration template file for Bppancestor.

• template_bppml_config_file.conf: Configuration template file for Bppml.

• tree_for_simulations.txt: Simulated dataset input tree file.

• tree_for_domains.txt: Pfam domain content reconstruction input tree file.