ClonalFrame(1)

✨ ClonalFrame(1) — General Commands Manual 💖

🦋 NAME

ClonalFrame — okay so this is the tool for inference of bacterial microevolution using multilocus sequence data 🧬✨

💅 SYNOPSIS

ClonalFrame [OPTIONS] inputfile outputfile

🌸 DESCRIPTION

Bestie, ClonalFrame is literally obsessed with figuring out which members of a sample are clonally related 💜 It also estimates where on the chromosome homologous recombination events happened, the ones that messed up the clonal inheritance. Main character energy fr 👑

Options:

• -x NUM — sets the number of iterations after burn-in (default is 50000) 🔥
• -y NUM — sets the number of burn-in iterations (default is 50000) 🎀
• -z NUM — sets the number of iterations between samples (default is 100) 🌈
• -e NUM — sets the number of branch-swapping moves per iterations (default is so that half of the time is spent branch-swapping) 🦋
• -m NUM — sets the initial value of theta to NUM (default is Watterson estimate) ✨
• -d NUM — sets the initial value of delta to NUM (default is 0.001) 🍓
• -n NUM — sets the initial value of nu to NUM (default is 0.01) 🧚
• -r NUM — sets the initial value of R to NUM (default is initial theta/10) 💫
• -M — do update the value of theta 💜
• -D — do not update the value of delta 🙈
• -N — do not update the value of nu 🙈
• -R — do not update the value of R 🙈
• -T — do not update the topology 🙈
• -A — do not update the ages of the nodes 🙈
• -G — remove all gaps 🫶
• -H — remove all gaps at non-polymorphic positions 🫶
• -t NUM — indicate which initial tree to use: 0 for a null tree, 1 for a uniformly chosen coalescent tree and 2 for UPGMA tree (default) 🌳
• -w FILE — use Newick file for initial tree 📜
• -a NUM — sets the first parameter of the beta prior distribution of nu 💖
• -b NUM — sets the second parameter of the beta prior distribution of nu 💖
• -U — use uniform priors for rho, theta and delta 🌸
• -B — run in BURST mode 💥
• -C — run in UPGMA mode with a site-by-site bootstrap procedure 🧁
• -c — run in UPGMA mode with a fragment-by-fragment bootstrap procedure 🧁
• -S NUM — sets the seed for the random number generator to NUM 🎲
• -E NUM — sets the rate of exponential growth (default is 0) 📈
• -I — ignores first block in the alignment 🙅‍♀️
• -L — clean-up the alignment before running ClonalFrame 🧹
• -l — minimum distance between two reference sites (default is 50) 📏
• -v — verbose mode, so you can see all the tea ☕

🎀 AUTHOR

ClonalFrame was written by Xavier Didelot. 👑

This manual page was written by Andreas Tille <tille@debian.org>, for the Debian project (but may be used by others). 🫶

Bestie, that's the whole tea ☕💖 This page is from the General Commands Manual and the version is 1.2, dated February 2011 🌸 Love you, go be iconic 🦋✨