These are scripts used to assemble data and analyze gene expression evolution in 'The evolution of gene expression underlying vision loss in cave animals'

• fasta2tree_w.py Takes a directory of fasta files, aligns them using translatorX, and estimates a tree using raxml, partitioned by codon. Alternatively, can specify to use iqtree with modeltesting. Need to adjust translatorx script path and raxml command. Needs mafft in the PATH

• get_cds_from_orthofinder.py Creates a fasta file for each orthogroup. Requires a concatenated cds file of all species and the Orthogroups.txt output from Orthofinder

• get_expression_data_from_orthofiner.py pulls and renames isoform expression levels from RSEM output for orthogroups in the OrthoFinder Orthogroups.txt file

• get_gene_trans_map.py Creates a tab delimited gene-transcipt map file from a Trinity assembly

• get_longest_protein_seq_per_orthogroup.py Loops through orthogroup fasta files and pulls the longest protein sequence in each from a concatenated sequence file

• get_reference_transcripts_from_orthofinder_orthogroups.py Creates a 'transcriptome' assembly file for each species with sequences renamed to orthogroups

• make_data_matrices_ouwie.py Takes an expression matrix and a .csv file with species states and creates an OUwie input file for each orthogroup

• run_ouwie.R Scripts to run OUwie on each orthogroup

• The data directory contains a species phylogeny, normalized expression matrix and 'states.csv' file with 'blind/sighted' designation for the 14 species (34 individuals)

Species Key
CCRYP - Cambarus cryptodytes
CDUBI - Cambarus dubius
CGRAY - Cambarus graysoni
CHAMU - Cambarus hamulatus
CNERT - Cambarus nerterius
CRUST - Cambarus rusticiformis
CSETO - Cambarus setosus
CTENE - Cambarus tenebrosus
OAUST - Orconectes australis
OINCO - Orconectes incomptus
PFALL - Procambarus fallax
PHORS - Procambarus horsti
PLUCI - Procambarus lucifugus
PPALL - Procambarus pallidus