primeDTLSR(1)

✨ NAME ✨

primeDTLSR — guest-in-host tree inference tool 🧚🦋

yep, we're in section 1, the General Commands Manual, and this is the one that does reconciliation. periodt.

💅 SYNOPSIS 💅

primeDTLSR [OPTIONS] seqfile hostfile [gsfile]

🌸 DESCRIPTION 🌸

okay so primeDTLSR is the guest-in-host tree inference tool, and what it does is enable reconciliation analysis using the underlying DTLRS model. Here's the model's whole vibe, bestie:

1. The guest tree topology evolves inside the host tree by means of duplication, loss and horizontal transfer events, all guided by homogeneous rates — much like a birth-death process, no cap. Lineages branch deterministically at host tree nodes.
2. Relaxed molecular clock ⏰ — that's sequence evolution rate variation over guest tree edges. Rates are drawn iid from the specified distribution. Also, rate variation over sites may be added, using a discretized gamma distribution with mean 1.
3. Substitution model of choice; standard or user-defined. The implementation uses a discretization of the host tree to approximate the probability of all possible reconciliation realizations for the current parameter state.

And she said it twice, so you KNOW it matters: the implementation uses a discretization of the host tree to approximate the probability of all possible reconciliation realizations for the current parameter state. 💅

Now the three positional args, and yes you need to know all of them:

• seqfile — the file with aligned sequences for guest tree leaves. 🌱
• hostfile — a PrIME Newick file with the host tree, incl. divergence times. > Heads up: leaves must have time 0 and the root must have time > 0. Not negotiable, bestie.
• gsfile — a tab-delimited file relating guest tree leaves to host tree leaves, in case that info isn't included in hostfile.

🎀 OPTIONS 🎀

• -h, -u, -? — display help (this text, literally).
• -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 [blank in the source, ngl].
• -t UNSIGNED_INT — thinning, i.e. sample every <value>-th iteration. Defaults to [also blank 🙈].
• -w UNSIGNED_INT — output diagnostics to stderr every <value>-th sample. Defaults to [blank again, she's mysterious].
• -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 [blank].
• -Sm UniformAA|JC69|JTT|UniformCodon|ArveCodon — substitution model. [blank] 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. > 🚨 Don't use both option -Su and -Sm at the same time.
• -Sn UNSIGNED_INT — number of steps of the discretized Gamma-distribution for sequence evolution rate variation over sites. Defaults to [blank] (which means no variation).
• -Ed Gamma|InvG|LogN|Uniform — distribution for IID rate variation among edges. Defaults to [blank].
• -Ep FLOAT FLOAT — initial mean and variance of the edge rate distribution. Defaults to [blank] and [blank].
• -Ef — fix mean and variance of the edge rate distribution. Non-fixed by default.
• -Gi FILE — filename with the initial guest tree topology.
• -Gg — fix the initial guest tree topology, i.e. perform no branch-swapping. Non-fixed by default.
• -Bp FLOAT FLOAT FLOAT — initial duplication, loss and transfer rates. Defaults to [blank], [blank] and [blank].
• -Bf — fix duplication, loss and transfer rates to their initial values. Non-fixed by default.
• -Bt FLOAT — override the time span of the edge above the root in the host tree. Must be greater than 0. Defaults to the file-contained value.
• -Dt FLOAT — approximate discretization timestep. Set to 0 to divide edge generations into the same amount of parts (see -Di). Defaults to [blank].
• -Di UNSIGNED_INT — minimum number of discretization subintervals per edge generation. If -Dt is set to 0, this becomes the exact number of subintervals. Minimum 2. Defaults to conf_value_from_cmake_DiscMinIvs (yep, that's the literal placeholder text, she left it un-substituted 💀).
• -C UNSIGNED_INT — number of transfer counts during sampling. Defaults to [blank].
• -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.
• -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.

🫶 EXIT STATUS 🫶

• 0 — successful program execution. slay. ✨
• 1 — some error occurred. 😭

🌈 URL 🌈

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

👑 SEE ALSO 👑

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

and that's the whole page, bestie 💖 this one's from prime-phylo 1.0.11, dated 13 Mar, 2012 — old but iconic, fr fr. go infer some trees 🦋🌸