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Supplemental Information

Table 1: The nine Alzheimer Disease genes used in the study.

DOI: 10.7287/peerj.preprints.230v1/supp-1

Table 2: The 34 species identified by ASAP2 using Alzheimer Disease gene queries.

DOI: 10.7287/peerj.preprints.230v1/supp-2

Table 3: Nucleotide PBS values for each internal node on nucleotide simultaneous analysis tree for each data partition.

DOI: 10.7287/peerj.preprints.230v1/supp-3

Table 4: Protein PBS values given for each internal node on protein simultaneous analysis tree for each data partition.

DOI: 10.7287/peerj.preprints.230v1/supp-4

Table 5: RF and RF′ distance between each pair of trees for nucleotide sequence data partitions.

DOI: 10.7287/peerj.preprints.230v1/supp-5

Table 6: RF and RF′ distance between each pair of trees for protein sequence data partitions.

DOI: 10.7287/peerj.preprints.230v1/supp-6

Table 7: RF and RF’ values between corresponding nucleotide and protein trees for each gene.

DOI: 10.7287/peerj.preprints.230v1/supp-7

Figure 1: Overview of ASAP2.

DOI: 10.7287/peerj.preprints.230v1/supp-8

Figure 2: Nucleotide Trees.

DOI: 10.7287/peerj.preprints.230v1/supp-9

Figure 4: Nucleotide Simultaneous Analysis Tree with Support Values.

DOI: 10.7287/peerj.preprints.230v1/supp-11

Figure 4: Protein Simultaneous Analysis Tree with Support Values.

DOI: 10.7287/peerj.preprints.230v1/supp-12

Figure 6a: Phylogenetic Network Based on Nucleotide Trees.

DOI: 10.7287/peerj.preprints.230v1/supp-13

Figure 6b: Phylogenetic Network Based on Protein Trees.

DOI: 10.7287/peerj.preprints.230v1/supp-14

All datafiles generated by ASAP2 for Alzheimer Disease.

DOI: 10.7287/peerj.preprints.230v1/supp-15

Additional Information

Competing Interests

The authors declare no competing interests.

Author Contributions

Joseph D Romano conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

William G Tharp conceived and designed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Indra N Sarkar conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding the deposition of related data:

https://github.com/JDRomano2/ASAP2/

Funding

The authors declare that there was no funding for this work The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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