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Updated Utilities (markdown)

Katzlab 2024-08-09 17:59:12 -04:00
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Utilities.md

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PhyloToL 6 includes a set of stand-alone utility scripts that aim to increase the power of the analysis done with or without the core PhyloToL pipeline. We divide these scripts into five main categories: assembly and fasta tools, sequence composition, MSA tools, gene tree descriptions and stand alone clade grabbing.
PhyloToL 6 includes a set of stand-alone utility scripts that aim to increase the power of the analysis done with or without the core PhyloToL pipeline. We divide these scripts into five main categories: assembly and fasta tools, sequence composition, MSA tools, gene tree descriptions and stand alone clade grabbing.
* assembly and fasta tools capture tasks including downloading sequences from GenBank, clustering sequences, calculating statistics on assemblies, and estimating most shared gene families (OGs) for use in PhyloToL part 2
All utilities are written in Python and contain headers that provide information on usage.
A summary of some of the scripts is divided by category here
All utilities are written in Python and contain headers that provide information on usage, and a summary of utilities is divided by category here
| Category | [Script name](https://github.com/Katzlab/PhyloToL-6/tree/main/Utilities) | Intent | Output |
| ----------------------------- | ------------------------------------------------------------------------ | ---------------------------------------------------------------------------------- | -------------------------------------------------------------------------- |