This fork of the data will be used in my gene expression adequacy project. I will assess the adequacy of the Ornstein-Uhlenbeck model for the dataset used in this paper
These are scripts used to assemble data and analyze gene expression evolution in 'The evolution of gene expression underlying vision loss in cave animals'
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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
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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
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get_expression_data_from_orthofiner.py pulls and renames isoform expression levels from RSEM output for orthogroups in the OrthoFinder Orthogroups.txt file
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get_gene_trans_map.py Creates a tab delimited gene-transcipt map file from a Trinity assembly
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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
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get_reference_transcripts_from_orthofinder_orthogroups.py Creates a 'transcriptome' assembly file for each species with sequences renamed to orthogroups
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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
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run_ouwie.R Scripts to run OUwie on each orthogroup
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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