README.md

See COMMANDLINES.md for command lines.

Scripts used for Kayal et al., in prep.

Char_map_5.11.R

R script used for stochastic character mapping

Cnid_only.nex

Tree in nexus format of all cnidarian sequences used in Char_map_5.11.R

LICENSE

License covering all scripts in this repository

NV_GO_Enrich_rels.R

R script used for GO enrichment analyses

PhyloBayesCATGTRI_OF75tx_1.treelist.pruned

PhyloBayes output before pruning Trichoplax

PhyloBayesCATGTRI_OF75tx_2.treelist.pruned

PhyloBayes output after pruning Trichoplax

all_scan.sh

Interproscan command lines

bilat_ai.fa.gz

FASTA file of cnidarian and bilaterian sequences. All our cnidarian sequences were BLASTed against this database. Definition lines of bilaterian sequences start with "ALIEN_ALIEN", a pattern, which is used by the program alien_index to flag sequences with better hits to bilaterian sequences. See: https://github.com/josephryan/alien_index and http://ryanlab.whitney.ufl.edu/downloads/alien_index/

colonial_charmatrix.txt

Character matrix for coloniality

get_fasta_w_min_number.pl

Perl script used to go through a set of FASTA files and print out those that have a certain number of FASTA sequences.

indorigin.dp.R

R script to test how many times a trait of interest was regained during evolution

medusa_charmatrix.txt

Character matrix for presence of medusa

overlay_3_23.R

part.txt

partitions from PartitionFinder

partition_comparison.R

R script to compare partitions

partition_finder.cfg

Configuration file used for partitionfinder run

plot_mat.R

polyp_charmatrix.txt

Character matrix for the presence of a polyp

scanNv.sh

command line for interproscan for N. vectensis

select_GO.sh

seq_processing.sh

Commands used for translating and further processing FASTA files

symbiont_charmatrix.txt

Character matrix for the presence of symbionts

venn.R

R script for generating venn diagram