primeDLRS(1)

💖 primeDLRS(1) 💖

General Commands Manual energy, bestie. Buckle up, this one's a whole vibe ✨

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🌸 NAME 🌸

primeDLRS, primeGSRf — the guest-in-host tree reconciliation tool 🦋

oh and btw, the old program name primeGSRf is still available — it's just a symlink to primeDLRS now, so if you type the old one, she'll answer 💅

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✨ SYNOPSIS ✨

primeDLRS [OPTIONS] seqfile hostfile [gsfile]

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👑 DESCRIPTION 👑

So this is the guest-in-host tree reconciliation tool, and she lets you analyse stuff like guest tree topologies, reconciliation properties, and duplication-loss rates. It's built on a Bayesian MCMC framework running the underlying GSR model. Periodt. 👑

Here's what's actually being modelled, in order:

1. the guest tree topology and its divergence times — modelled with a duplication-loss process in accordance with the Gene Evolution Model (GEM).
2. sequence evolution — modelled with a user-defined substitution model.
3. sequence evolution rate variation over guest tree edges (that's the relaxed molecular clock) — modelled with iid values from a user-selected distribution.
4. sequence evolution rate variation over sites (positions) — modelled according to a discretized Gamma distribution.

The implementation does its computations using a discretization of the host tree. And like, please actually read the options before you run this, because you will need to change default settings. Also, option -r may be useful to avoid numeric issues due to scaling — just saying 🫶

seqfile is a file with aligned sequences for guest tree leaves.

hostfile is a PrIME Newick file with the host tree incl. divergence times. Heads up: leaves must have time 0 and root must have time > 0 ⏰

gsfile is a tab-delimited file relating guest tree leaves to host tree leaves, if that info isn't already included in hostfile.

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🎀 OPTIONS 🎀

okay real talk: a bunch of these defaults are literally blank in the original doc — like it just says Defaults to . with nothing there 😭 that's not me skipping anything, that's what it says, iykyk.

• -h, -u, -? — Display help (this text). three whole ways to say "help me" 💀
• -o FILE — Output filename. Defaults to stderr.
• -s UNSIGNED_INT — Seed for the pseudo-random number generator. Defaults to a random seed.
• -i UNSIGNED_INT — Number of iterations. Defaults to .
• -t UNSIGNED_INT — Thinning, i.e. sample every <value>-th iteration. Defaults to .
• -w UNSIGNED_INT — Output diagnostics to stderr every <value>-th sample. Defaults to .
• -q — Do not output diagnostics. Non-quiet by default. 🤫
• -m MCMC|PDHC|PD — Execution type (MCMC, posterior density hill-climbing from initial values, or just initial posterior density). Defaults to .
• -Sm UniformAA|JC69|F81|JTT|UniformCodon|ArveCodon — Substitution model. . by default.
• -Su DNA|AminoAcid|Codon <Pi=float1 float2 ... floatn> <R=float1 float2 ...float(n*(n-1)/2)> — User-defined substitution model. The size of Pi and R must fit the data type (DNA: n=4, AminoAcid: n=20, Codon: n=62). R is given as a flattened upper triangular matrix. And don't use both option -Su and -Sm, bestie, pick a lane 🙈
• -Sn UNSIGNED_INT — Number of steps of discretized Gamma-distribution for sequence evolution rate variation over sites. Defaults to . (no variation).
• -Ed Gamma|InvG|LogN|Uniform — Distribution for iid sequence evolution rate variation over guest tree edges. Defaults to . (and no, do not confuse this with -Sn 😭).
• -Ep FLOAT FLOAT — Initial mean and variance of sequence evolution rate. Defaults to a simple rule-of-thumb based on host tree times.
• -Ef — Fix mean and variance of sequence evolution rate. Non-fixed by default.
• -Gi FILE — Filename with initial guest tree topology.
• -Gg — Fix initial guest tree topology, i.e. perform no branch-swapping. Non-fixed by default.
• -Gl — Fix initial guest tree edge lengths (in addition to topology), i.e. fix the edge lengths. Non-fixed by default.
• -Bp FLOAT FLOAT — Initial duplication and loss rates. Defaults to . and .
• -Bf — Fix initial duplication and loss rates. Non-fixed by default.
• -Bt FLOAT — Override time span of edge above root in host tree. If the value is <=0, the span will be set to equal the root-to-leaf time. Defaults to the value in the host tree file. See also option -Dtt.
• -Dt FLOAT — Approximate discretization timestep. Set to 0 to divide every edge in equally many parts (see -Di). Defaults to . See -Dtt for the edge above root.
• -Di UNSIGNED_INT — Minimum number of parts to slice each edge in. If -Dt is set to 0, this becomes the exact number of parts. Minimum 2. Defaults to . See -Dtt for the edge above root.
• -Dtt UNSIGNED_INT — Override number of discretization points for the edge above root in host tree. By default, irrespective of time span, this is set to the number of points for a (hypothetical) root-to-leaf edge
• -r — Rescale the host tree so that the root-to-leaf time equals 1.0. All inferred parameters will refer to the new scale. Off by default. Note that discretization parameters are NOT rescaled. ⚠️
• -Z — Do not print elapsed wall time and CPU time
• -W — Do not print the command line
• -debuginfo — Show misc. info to stderr before iterating. Not shown by default.

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💀 EXIT STATUS 💀

• 0 — Successful program execution. ate 💅
• 1 — Some error occurred 😭

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🌈 URL 🌈

The prime-phylo home page: http://prime.sbc.su.se

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🫶 SEE ALSO 🫶

primeDTLSR(1), primeGEM(1), showtree(1), chainsaw(1), reconcile(1), reroot(1), tree2leafnames(1), treesize(1)

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and that's the whole thing, bestie — this was prime-phylo version 1.0.11, dated 13 Mar, 2012 ✨ go reconcile some trees, you're gonna slay, mwah 💖🎀