DISPLAY_RATE_MATRIX(1)

✨ display_rate_matrix(1) ✨

okay bestie, so this is display_rate_matrix — a lil tool that lives in the PHAST suite 💖 it's the user-commands manual page, and she's here to show you matrices, no cap.

💅 NAME 💅

display_rate_matrix — this tool is part of the PHAST suite 🫶

🎀 OPTIONS 🎀

• -t <t> — instead of spitting out Q, output P(t) = exp(Qt) 🌸 and yes, it requires t >= 0. if you pass -t A she'll give you a matrix for each branch of the tree, iconic behavior fr fr.
• -f — show the equilibrium frequencies as an extra table row 👑 in list node they get shown with the first tuple being -.
• -e — show "exchangeabilities" instead of the raw matrix elements — that means dividing each element by the equilibrium frequency of its own column 💫 not available with -t, sorry babes.
• -d — suppress printing the elements on the main diagonal 🙈 we're gatekeeping those.
• -L — format the table for typesetting with LATEX ✨ incompatible with -l, pick a lane.
• -l — show matrix elements as a list instead of a table 📝 when -t is not specified (that's the rate matrix case), only the off-diagonal elements get printed.
• -i — (for use with -l only) report whether each substitution is a transition or a transversion 🧬
• -z — (for use with -l) report elements equal to zero 💀 they're omitted by default, except with -t. implied by -a.
• -S — (for use with -l) assume a symmetric matrix and report half as many lines 🦋 super useful with -e.
• -E — (for use with -l) print rates and probabilities in scientific notation — that's format %e instead of %f 🔬
• -a — (requires a model of order 3) replace a matrix of codon substitution rates with the induced matrix of amino acid substitution rates, according to the universal genetic code 🧚 see Yang, Nielsen, and Hasegawa, 1998.
• -s — (for use with -a) include stop codons 🛑 by default they're suppressed.
• -M <f> — (for use with -l only; implies -a) read an amino-acid substitution matrix from file <f> and report values from this matrix with the induced amino acid substitution rates 🌈 the matrix should be in the format used by BLAST (as produced by the NCBI "pam" program).
• -N <f> — like -M but for matrices in the format used by the PAML package for amino acid substitution and rate matrices 💜
• -A <f> — (for use with -l only and not with -M/-N) read alternative substitution scores from file <f> and report values in the output ⭐ file <f> should have three columns: a "from" tuple, a "to" tuple, and a real-valued score. substitutions that aren't listed get null scores and are reported as "NA".
• -B <f> — like -A but compares to rates of a single-nucleotide model (order 1) 🌸 file <f> should be a standard tree model (.mod) file.
• -C — report context-dependent transition/transversion rates, as shown in Tables 2 and 3 of Morton et al., JME 45:227-231, 1997 📚 requires a model of order 3 with a DNA alphabet.
• -h — print this help message 🫶

lowkey reminder bestie: some of these flags don't play nice together, so check the vibes (-e + -t? no. -L + -l? also no.) before you run her 💅

and that's the whole page!! this was display_rate_matrix version 1.4, dated May 2016 — slay, mwah, take care of her 💖✨🎀🦋