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Updated Utilities (markdown)

Adri K. Grow 2025-08-19 17:00:31 -04:00
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Utilities.md

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# Utilities summary
EukPhylo includes a set of stand-alone utility scripts that aim to increase the power of the analysis done with or without the core EukPhylo 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 EukPhylo 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.
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| | RenameTips.py | Renames the tip labels of trees to include metadata such as location and date | Renamed trees |
| | | | |
| Stand-alone clade grabbing | CladeGrabbing.py | Selects clades of interest from trees using taxonomic specifications | Phylogenetic trees |
# Using the Utilities (in progress of drafting)