Data and Supplement from: Phylogenetic tree instability after taxon addition: Empirical frequency, predictability, and consequences for online inference
Data files
Nov 01, 2024 version files 5.21 MB
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alignments.zip
5.21 MB
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README.md
2.31 KB
Abstract
https://doi.org/10.5061/dryad.63xsj3v9x
Description of the data and file structure
Alignments
This dataset of 1,000 nucleotide alignments is a subsample of the datasets presented by Harrington et al., 2021 (https://doi.org/10.5061/dryad.g4vp6jv, https://doi.org/10.5061/dryad.b568p21), which we converted to FASTA files. Originally, these datasets come from three sources:
- Brown and Thomson, 2017 (https://doi.org/10.1093/sysbio/syw101): Amniotes data containing gene sequences with small numbers of taxa (less than 50 taxa)
- we sampled 43 of these alignments
- Richards et al., 2018 (https://doi.org/10.1093/sysbio/syy013): mtDNA sequences of all 13 protein-coding mitochondrial genes of a variety of tetrapod species giving us alignments containing between 20 and 575 sequences
- we sampled 9 of these alignments
- Sanderson et al., 2009 (https://doi.org/10.1080/10635150802158688): datasets assembled by Harrington et al. (2021) from the PhyLoTA database, which contain nucleotide alignments with up to 250 sequences curated from GenBank with diverse taxon compositions and sizes.
- we sampled 948 of these alignments
Supplement
Additionally, we present the PDF of supplementary information for the article “Phylogenetic tree instability after taxon addition: empirical frequency, predictability, and consequences for online inference”.
Files and variables
File: alignments.zip
Description: Zipped directory of nucleotide alignments containing characters “A”, “C”, “G”, “T”, and “-“ in FASTA format.
File: supplement.pdf
Description: PDF containing supplementary materials and figures for the main article.
Access information
Data was derived from the following sources:
The dataset presented here is a subsample of 1,000 alignments of the datasets of Harrington et al.: https://doi.org/10.5061/dryad.g4vp6jv