Instructions to replicate analyses are provided here. ### 1. Get taxon names from fasta file ``` python Fasta_Get_Taxa.py -i /analysis/00_Starting_Data -o /analysis/01_Taxa_Assessment ``` The output was used to create the taxon list file called `Squamate-Taxon-List.txt`. ### 2. Parse loci The three required input files were placed in `/analysis/02-Starting-Materials`: + **Locus search terms**: `Locus-Search-Terms-UCE-5k-SquamateCoords.txt` + **Taxon list**: `Squamate-Taxon-List.txt` + **Starting sequences**: `Squamate-UCEs_NCBI_Genome_Published.fasta` + ``` python Parse_Loci.py -i /analysis/02-Starting-Materials/Squamate-UCEs_NCBI_Genome_Published.fasta -o /analysis/03_Parse_Loci -l /analysis/02-Starting-Materials/Locus-Search-Terms-UCE-5k-SquamateCoords.txt -t /analysis/02-Starting-Materials/Squamate-Taxon-List.txt ``` ### 3. Adjust sequence directions ``` python Adjust_Direction.py -i /analysis/03_Parse_Loci/Parsed-Fasta-Files -o /analysis/04_Adjust --threads 8 ``` ### 4. Filter by minimum sequence number ``` python Fasta_Filter_by_Min_Seqs.py -i /analysis/05_Adjust/Adjusted-Fasta-Files -o /analysis/06_Min_Taxa --min_seqs 10 ``` ### 5. Sequence alignment The alignment module was run four times, one for each alignment method. **MAFFT-Acc**: ``` python Align.py -i /analysis/06_Min_Taxa/Filtered-Fasta-Files -o /analysis/07_Align -a mafft --threads 8 --accurate ``` **MAFFT-Auto**: ``` python Align.py -i /analysis/06_Min_Taxa/Filtered-Fasta-Files -o /analysis/07_Align -a mafft --threads 8 ``` **Muscle**: ``` python Align.py -i /analysis/06_Min_Taxa/Filtered-Fasta-Files -o /analysis/07_Align -a muscle ``` **Clustal-O**: ``` python Align.py -i /analysis/06_Min_Taxa/Filtered-Fasta-Files -o /analysis/07_Align -a clustalo ``` ### 6. Relabel sequences Sequences were relabeled for each of the outputs above using the basic command: ``` python Fasta_Relabel_Seqs.py -i [alignments folder] -o /analysis/08_Relabel -r species ``` ### 7. Trim alignments Two trimming methods were run per alignment set using the general commands below. **Gap-threshold trimming** ``` python Trim_Alignments_Trimal.py -i [alignment fasta set] -o [output directory] -fasta -a gt --gt 0.2 ``` **Gappyout trimming** ``` python Trim_Alignments_Trimal.py -i [alignment fasta set] -o [output directory] -fasta -a gappyout ``` ### 8. Convert format Each set of trimmed fasta files was converted to phylip and nexus using the general command below: ``` python Fasta_Convert.py -i [input directory] -o [output directory] ``` ### 9. Concatenate Each set of trimmed fasta files was concatenated using the general command below: ``` python /Users/portik/Documents/GitHub/SuperCRUNCH/supercrunch-scripts/Concatenation.py --informat phylip --outformat phylip -s dash -i [input directory of fasta files] -o [output directory] ```