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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.
* 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
* sequence composition analysis calculates statistics for coding domains (e.g. composition, effective number of codons), plots outputs, and enables users to rename sequences in "ready to gos" based on GC content at silent sites.
* MSA tools include assessment of gaps, a wrapper for Guidance analyses, and a tool to count taxa across gene families (useful for deciding on which trees to run after part 1
* Gene tree description utilities allows users to modify trees (i.e. to rename and color tips) and to assess clade sizes and levels of contamination
* Stand-alone clade grabbing allows users to select sequences from robust clades based on user defined rules
All utilities are written in Python and contain headers that provide information on usage, and a summary of utilities is divided by category here