INDELIBLE(1)

💖 INDELIBLE(1) 💖

okay bestie, sit down, hydrate, and let me tell you about indelible — a powerful and flexible simulator of biological evolution. it's giving lab-girlie main character energy, fr fr 🧬✨

✨ SYNOPSIS ✨

indelible

that's it. that's the whole thing. No options can be passed via the commandline. 💅

🦋 DESCRIPTION 🦋

so indelible can simulate evolution of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time. and the way that it supports all common evolutionary models?? obsessed. 🔥

The full documentation for indelible is available under /usr/share/doc/indelible/help/index.html. go read it, it's iconic, iykyk 📖💖

🎀 CONFIGURATION 🎀

indelible reads the settings for a simulation run from a file named control.txt in the current directory. yes bestie, the current directory, no you can't argue with it.

The file is split into blocks, with each block controlling one particular aspect of the simulation. Blocks may contain further sub-blocks. Comments can be given in C or C++ style. (very retro of them but we respect it 🙈)

🫶 heads up: if indelible is executed without a control file present, an example file is generated. free starter pack, we love a generous king.

• [TYPE] type — Every control file must begin with a TYPE block, no skipping, no exceptions, periodt. The possible types are NUCLEOTIDE, AMINOACID, and CODON.
• [SETTINGS] — This block specifies non-essential user preferences such as output file types and formats, seeds for the random number generator, and whether to output detailed reports.
• [MODEL] modelname — This block starts a new evolutionary model to be used for simulation. The particular parameters including substitution models, indel-rates and codon-site models are controlled via submodels. modelname can be any name of your choosing. (name it after your cat, we support that 💜)
• [TREE] treename newick — This block is used to specify a guide-tree with the given name treename. Evolutionary distances are represented as branch lengths for the tree in NEWICK format.
• [BRANCHES] — These blocks are used to simulate non-stationary and non-homogenous processes. Different models can be specified on different branches of the guide-tree allowing branches to have different models of substitution, indel length distribution, rate heterogeneity, base composition etc. literally the glow-up block 🌈
• [PARTITIONS] partitionname — During each run multiple sequence partitions can be simulated. For each partition the guide-tree, evolutionary model and sequence length has to be specified.
• [EVOLVE] — Within this block multiple replicas of a partition may be generated. ✨

👑 COPYRIGHT 👑

Copyright © 2010 William Fletcher License GPLv3+: GNU GPL version 3 or later.

This is free software: you are free to change and redistribute it.

🚨 There is NO WARRANTY, to the extent permitted by law. read it and weep (affectionately). 🚨

The full license text is available at <http://gnu.org/licenses/gpl.html>.

🌸 ACKNOWLEDGMENTS 🌸

William Fletcher and Ziheng Yang (2009). INDELible: A Flexible Simulator of Biological Sequence Evolution, Molecular Biology and Evolution, 26(8):1879-1888. cite your sources besties, it's the bare minimum 💅📚

and that's the whole page babes 💖 this was version 1.03, dated 2010, and it's INDELIBLE(1) — go forth and simulate, you absolute legend 🦋✨💜