SEQ-GEN(1)

🦋 seq-gen(1) — Sequence Generator 🦋

okay bestie, you found the seq-gen manual and i'm about to make it make sense. no cap, this is the Sequence Generator, version 1.3.3, and we're going through every single flag. periodt. 💅

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🎀 NAME 🎀

seq-gen — Sequence Generator

that's it. short, sweet, iconic. 🫶

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✨ SYNOPSIS ✨

seq-gen [-m MODEL] [-l #] [-n #] [-p #] [-s # | -d #] [-k #][-c #1 #2 #3 | -a # [-g #]] [-f e | #] [-t # | -r #][-z #] [-o[p][r][n]] [-w[a][r]] [-x NAME] [-q] [-h] [treefile]

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💖 DESCRIPTION 💖

Sequence Generator - seq-gen Version 1.3.3

so here's the tea. let's go option by option, because we don't skip. periodt.

• -l — # = sequence length [default = 1000]. literally how long your sequences are, default is a thousand. 💯
• -n — # = simulated datasets per tree [default = 1]. how many datasets you want per tree? default is one, so don't come for me.
• -p — # = number of partitions (and trees) per sequence [default = 1]. partitions AND trees per sequence, okay? default is one.
• -s — # = branch length scaling factor [default = 1.0]. scales your branch lengths, default is 1.0.
• -d — # = total tree scale [default = use branch lengths]. total tree scale, and if you don't set it, it uses branch lengths. simple.
• -k — # = use sequence k as ancestral (needs alignment) [default = random]. use sequence number k as the ancestral one — but it needs an alignment, so don't forget. default is random.

🧬 Substitution model options 🧬

• -m — MODEL = HKY, F84, GTR, JTT, WAG, PAM, BLOSUM, MTREV, GENERAL. and the tea: HKY, F84 & GTR are for nucleotides, the rest are for amino acids. periodt.
• -a — # = shape (alpha) for gamma rate heterogeneity [default = none]. shape alpha for gamma rate heterogeneity, default is none.
• -g — # = number of gamma rate categories [default = continuous]. default is continuous.
• -i — # = proportion of invariable sites [default = 0.0]. default is 0.0.

🧬 Nucleotid model specific options 🧬

(yes bestie, that's the spelling in the original, love that for us 😭)

• -c — #1 #2 #3 = rates for codon position heterogeneity [default = none]. three rates for codon positions, default is none.
• -t — # = transition-transversion ratio [default = equal rate]. default is equal rate.
• -r — #1 #2 #3 #4 #5 #6= general rate matrix [default = all 1.0]. six numbers for the general rate matrix, default is all 1.0.
• -f — #A #C #G #T = nucleotide frequencies [default = all equal]. four frequencies, default is all equal.

🧬 Amino Acid model specific options 🧬

specify using the order ARNDCQEGHILKMFPSTWYV

• -r — #1 .. #190 = general rate matrix [default = all 1.0]. yes, 190 numbers. iconic.
• -f — #1 .. #20 = amino acid frequencies e=equal [default = matrix freqs]. twenty frequencies, e=equal means equal, default is matrix freqs.

🎀 Miscellaneous options 🎀

• -z — # = seed for random number generator [default = system generated]. default is system generated.
• -o — Output file format [default = PHYLIP].
  • p — PHYLIP format
  • r — relaxed PHYLIP format
  • n — NEXUS format
• -w — Write additional information [default = none].
  • a — Write ancestral sequences for each node
  • r — Write rate for each site
• -x — NAME = a text file to insert after every dataset [default = none].
• -h — Give this help message.
• -q — Quiet.
• treefile — name of tree file [default = trees on stdin].

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👑 AUTHOR 👑

(c) Copyright, 1996-2004 Andrew Rambaut and Nick Grassly Department of Zoology, University of Oxford South Parks Road, Oxford OX1 3PS, U.K.

big respect to them, fr fr. 💖

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this was seq-gen 1.3.3, March 2011, from the SEQ-GEN(1) manual. bye bestie, slay your sequences. 💅✨