<filename>tex/manuscripts/ecoevolity/tables/ipyrad-settings.tex
\begin{table}[htbp]
\sffamily
\captionsetup{name=Table S, labelformat=noSpace}
\caption{
    Settings used for assembling loci for each pair of gekkonid populations.
}
\centering
\begin{tabular}{ l l }
    \textbf{ipyrad setting} & \textbf{Value} \\
    \hline
    assembly\_method & denovo \\
    datatype & rad \\
    restriction\_overhang & TATG, \\
    max\_low\_qual\_bases & 4 \\
    phred\_Qscore\_offset & 33 \\
    mindepth\_statistical & 6 \\
    mindepth\_majrule & 6 \\
    maxdepth & 10000 \\
    clust\_threshold & 0.85 \\
    max\_barcode\_mismatch & 0 \\
    filter\_adapters & 1 \\
    filter\_min\_trim\_len & 35 \\
    max\_alleles\_consens & 2 \\
    max\_Ns\_consens & 4 \\
    max\_Hs\_consens & 5 \\
    min\_samples\_locus & 4 \\
    max\_SNPs\_locus & 20 \\
    max\_Indels\_locus & 8 \\
    max\_shared\_Hs\_locus & 0.5 \\
    trim\_reads & 0, 0, 0, 0 \\
    trim\_loci & 0, 0, 0, 0 \\
    \hline
\end{tabular}
\label{table:ipyradsettings}
\end{table}

