Heat_shock_protein_selection_analysis

Software versions used: Orthofinder (version 2.3.14) MAFFT (version 7.511ma) PAL2NAL (version 14) IQTREE (version 8.2.12), HYPHY (2.5.33)

Name		Name	Last commit message	Last commit date
Latest commit History 10 Commits
1st_filt.py		1st_filt.py
Data_Manipulation.ipynb		Data_Manipulation.ipynb
Extract_Outgroups.ipynb		Extract_Outgroups.ipynb
Fasta_duplicate_sequence_filter.py		Fasta_duplicate_sequence_filter.py
Fix_headers_by_adding_species_name.ipynb		Fix_headers_by_adding_species_name.ipynb
Get_Orthogroups.ipynb		Get_Orthogroups.ipynb
HSP_Orthogroups.zip		HSP_Orthogroups.zip
Isolates_experimental_sequences.ipynb		Isolates_experimental_sequences.ipynb
OG0006156.fasta.BUSTED.png		OG0006156.fasta.BUSTED.png
OG0006156.fasta.MEME.json.png		OG0006156.fasta.MEME.json.png
OG0006156.fasta.MEME.json.tree.png		OG0006156.fasta.MEME.json.tree.png
README.md		README.md
Taxonomy.csv		Taxonomy.csv
cds.srun		cds.srun
cds_master_script.py		cds_master_script.py
cds_master_script_all_fish.py		cds_master_script_all_fish.py
cds_orthologs.py		cds_orthologs.py
cds_to_orthogroup.py		cds_to_orthogroup.py
change_cds_headers.ipynb		change_cds_headers.ipynb
concat.py		concat.py
hsps_70.csv		hsps_70.csv
hyphy.py		hyphy.py
hyphy.srun		hyphy.srun
hyphy_meme.py		hyphy_meme.py
hyphy_meme.srun		hyphy_meme.srun
macse_python_use_this_one.py		macse_python_use_this_one.py
mass_iqtree.py		mass_iqtree.py
mass_iqtree_no_outgroup.py		mass_iqtree_no_outgroup.py
mass_mafft_auto.py		mass_mafft_auto.py
ortho_hpc.bash		ortho_hpc.bash
rename_fasta_headers.py		rename_fasta_headers.py
updated_cds_to_orthogroup.py		updated_cds_to_orthogroup.py

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