diff --git a/Utilities.md b/Utilities.md index 280bc04..5387bef 100644 --- a/Utilities.md +++ b/Utilities.md @@ -1,8 +1,8 @@ -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 | | ----------------------------- | ------------------------------------------------------------------------ | ---------------------------------------------------------------------------------- | -------------------------------------------------------------------------- |