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Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?
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Welcome! Here you can find all the data and instructions required to reproduce the analyses in the following paper:
- Portik, D.M., and J.W. Wiens. 2021. Do alignment methods matter for phylogenomic (UCE) analyses? Systematic Biology, 70: 440–462.
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Components
UCE Sequences
UCE sequence data obtained from GenBank, published genomes, and supplementary materials of published studies. Includes all sequences for birds, squama...
Final Alignments
The complete set of alignments for all 12 alignment-trimming combinations for birds, squamates, and tetrapods.
SuperCRUNCH Analysis: Squamates
Complete instructions, along with inputs and outputs, for the SuperCRUNCH analysis of squamates.
SuperCRUNCH Analysis: Birds
Complete instructions, along with inputs and outputs, for the SuperCRUNCH analysis of birds.
SuperCRUNCH Analysis: Tetrapods
Complete instructions, along with inputs and outputs, for the SuperCRUNCH analysis of tetrapods.
Phylogenetic Results and MonoPhylo Summaries
Tree files for the concatenated RAxML and ASTRAL-III analyses of the squamate, bird, and tetrapod datasets. Includes RAxML gene trees and MonoPhylo su...
Subsampling Analyses
Subsampling analyses for squamates, birds, and tetrapods. Includes concatenated RAxML and ASTRAL-III trees for all replicates, along with MonoPhylo su...
ASL-CV Analyses
Results of the Aligned-Sequence-Length Coefficient of Variation (ASL-CV) Analyses for Birds, Squamates, and Tetrapods.
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