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Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses? /
SuperCRUNCH Analysis: Birds
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Category: Analysis
Description: Complete instructions, along with inputs and outputs, for the SuperCRUNCH analysis of birds.
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 Bird-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-set.…
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