# Pilot HybSeq ### Trim With Fastp default parameters ### Assemble with HybPiper default parameters run stats script run heatmap script run retrieve sequences ```bash= hybpiper retrieve_sequences dna -t_dna cycad333_targets.fasta --sample_names namelist.txt --fasta_dir FNA ``` ### Align with MAFFT ```bash= parallel -j 20 --eta "mafft --preservecase --auto FNA/{}.FNA > mafft/{}.mafft.fasta" :::: genelist.txt ``` ### Trim with TrimAl ```bash= parallel -j 20 trimal -in mafft/{}.mafft.fasta -out trimal/{}.trimal.fasta -gt 0.5 :::: genelist.txt ``` ### Gene trees with iqtree ```bash= parallel -j 5 --eta iqtree -s {}.trimal.fasta -T 4 -B 1000 -m MFP :::: ../genelist.txt ``` ### Species tree with astral ```bash= cat trimal/*.treefile > astral/cycad.genetrees.tre astral -i cycad.genetrees.tre -o cycad.astral.tre ``` ## ToDo ### Rerun without the definitely bad samples exon and supercontig ### Population Genomics: Encephalartos horrida and Cycas platyphylla Just need the SNP diversity, heterozygosity, Ne, for 10-15 individuals, 5 per populations