DOI: 10.5061/dryad.sbcc2fr85
title: Supplementary data for: DNA sequences are as useful as protein sequences for inferring deep phylogenies

description: Inference of deep phylogenies has almost exclusively used protein rather
 than DNA sequences, based on the perception that protein sequences are
 less prone to homoplasy and saturation or to issues of compositional
 heterogeneity than DNA sequences. Here we analyze a model of codon
 evolution under an idealized genetic code and demonstrate that those
 perceptions may be misconceptions. We conduct a simulation study to assess
 the utility of protein versus DNA sequences for inferring deep
 phylogenies, with protein-coding data generated under models of
 heterogeneous substitution processes across sites in the sequence and
 among lineages on the tree, and then analyzed using nucleotide, amino
 acid, and codon models. Analysis of DNA sequences under
 nucleotide-substitution models (possibly with the third codon positions
 excluded) recovered the correct tree at least as often as analysis of the
 corresponding protein sequences under modern amino acid models. We also
 applied the different data-analysis strategies to an empirical dataset to
 infer the metazoan phylogeny. Our results from both simulated and real
 data suggest that DNA sequences may be as useful as proteins for inferring
 deep phylogenies and should not be excluded from such analyses. Analysis
 of DNA data under nucleotide models has a major computational advantage
 over protein-data analysis, potentially making it feasible to use advanced
 models that account for among-site and among-lineage heterogeneity in
 the nucleotide-substitution process in inference of deep
 phylogenies.
description: The repository includes scripts, control files and empirical data
 used in the "Kapli P., Kotari I., Telford M., Goldman N., Yang Z. DNA
 Sequences Are as Useful as Protein Sequences for Inferring Deep
 Phylogenies." manuscript.
description: Supplementary data for the manuscript:<br>Kapli P., Kotari
 I., Telford M., Goldman N., Yang Z. DNA Sequences Are as Useful as Protein
 Sequences for Inferring Deep Phylogenies. Brief
 explanations of the files: The script
 "convert.py" takes as input a codon alignment and outputs the
 equivalent amino acid and the DNA alignment of the 1st and 2nd codon
 positions. The "HOMO-control.txt" is the
 control file for simulating sequences under the homogeneous model with
 indelible (http://abacus.gene.ucl.ac.uk/software/indelible/). All guide
 trees and model parameters (M0 and M3) are provided in the
 file. The "SH1-control.txt" is the control
 file for simulating sequences under the site-heterogeneous (SH1) model.
 SH1 assumes site-heterogeneous codon frequencies generated from observed
 frequencies in coding genes from mammal species. All guide trees and model
 parameters (M0 and M3) are provided in the file. The
 two Python scripts: "generate_control_M0_SH2.py" and
 "generate_control_M3_SH2.py" create control files for indelible
 with the SH2 model. In particular, it converts the amino acid frequencies
 from the mixture models C10-C60 into equivalent codon frequencies, i.e.
 the frequency of each codon is calculated by the frequency of the amino
 acid divided by the number of synonymous codons for the amino acid and
 multiplied by the nucleotide frequency for the nucleotide at the 3rd codon
 position. It then formats the indelible control file accordingly. All
 guide trees are available in each of the scripts. 
 Syntax for running the script:<br>./generate_control_M[0 or
 3].py [AA mixture model: C10-C60] [frequency C] [frequency T] [frequency
 A] [ALIGNMENT LENGTH] An example output of the
 generate_control_M0.py is also provided:
 example_control_file_SH2.txt. The
 equivalent scripts "generate_control_M3_BSH.py" and
 "generate_control_M3_BSH.py" as in SH2 but for the branch-site
 model. Syntax for running the
 script:<br>./generate_control_M[0 or 3].py [AA mixture model:
 C10-C60] [frequency C 1] [frequency T 1] [frequency A 1] [frequency C 2]
 [frequency T 2] [frequency A 2] [ALIGNMENT LENGTH] The
 two sets of frequencies are assigned to different parts of the
 tree. For the metazoa analyses the
 following files are included: 1)
 "metazoa_alignment.CODONS.clean2.fasta.tar.gz" the DNA alignment
 for the 22 animal species used in the study, and 2) two scripts:
 "generate_control_M3_BSH-metazoa.py" and
 "generate_control_M3_SH2-metazoa.py" that generate indelible
 control files under the BSH and the SH2 models correspondingly and with
 guide trees matching the metazoa phylogenies A and C of Figure 3 in the
 manuscript.