Supplementary Material: Are the Heteromyidae paraphyletic? Molecular phylogenetics of extant geomyoid rodents

<br><b>Description of the data and file structure</b><i>Are the Heteromyidae paraphyletic? Molecular phylogenetics of extant geomyoid rodents</i>Enrique P. Lessa* and Andrés ParadaDepartamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República. Iguá 4225, Montevideo 11400, Uruguay. E-mail: [e-mail] (EPL); [e-mail] (AP).*Corresponding author: Enrique P. LessaFiles<b>Supplementary Table 1</b>Table containing accession number for the mitochondrial data, mitochondrial dataset stats, partition scheme and substitution model for each loci, UCE dataset stats, partition scheme and substitution model for each loci and Summary stats for each dataset<br><b>Mitochondrial Dataset</b>File: Mitochondrial.zip<b>Description:</b> The analysis of 2 mitochondrial dataset was conducted as follows:Mitochondrial dataset: the 13 protein-coding mitochondrial DNA genes (for 13 species).Mitochondrial dataset: matrix of 12s, 16s, and COX1 loci (for 43 species).Mitochondrial.zip contains the following files:Archives with the extension .fas, .part and .tree denote the alignment, the partition file and the best tree with support for this datasets<b>Ultraconserved Elements</b>File: IQ-TREE.zip<b>Description:</b> The analysis of 2 ultraconserved elements dataset was conducted as follows:Ultraconserved dataset: a matrix of 3991 loci, allowing for up to 2 taxa missing per locus (for 9 species).Ultraconserved dataset: a matrix of 1750 loci (no missing data).The IQ-TREE.zip file contains the results of the concatenated approach.Archives with the extension .fas, .part and .tree denote the alignment, the partition file and the best tree with support for this datasetsThe ASTRAL.zip file contains the results of the coalescent approach.Archives with the extension .trees contain the topologies searched.File: ASTRAL.zip<b>Description:</b>The topology of either the 1750 or 3991 dataset are identical. ASTRAL_3991_SCORED.tree is the species tree recovered with ASTRAL and the associated node support.<b>Individual Alignments</b>Each alignment can be reconstructed splitting the .fas file with a tool such as AMAS and omitting the first column of the partition file e.g.<pre><pre>awk '{ print $2" "$3" "$4}' mito13x13.part &gt; AMAS-mito13x13.part<br>conda create -n amas python=3 pipconda activate amas<br>pip install amas<br>gh repo clone marekborowiec/AMAS<br>python ./AMAS/amas/AMAS.py split -f fasta -d dna -i mito13x13.fas -l AMAS-mito13x13.part -u fasta</pre></pre>