From ecad962b77d749c0ae9f464cb94255195d15b0f8 Mon Sep 17 00:00:00 2001
From: "Adri K. Grow" <42044618+adriannagrow@users.noreply.github.com>
Date: Tue, 19 Aug 2025 17:00:31 -0400
Subject: [PATCH] Updated Utilities (markdown)

---
 Utilities.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/Utilities.md b/Utilities.md
index 80e72e4..68c435e 100644
--- a/Utilities.md
+++ b/Utilities.md
@@ -1,3 +1,4 @@
+# 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.
@@ -36,4 +37,6 @@ All utilities are written in Python and contain headers that provide information
 |                               | ContaminationBySisters.py                                           | Summarizes the taxonomic distribution of sister sequences for each taxon in a tree | Two spreadsheets summarizing tree tips relationship                        |
 |                               | 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                                                         |
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+| Stand-alone clade grabbing    | CladeGrabbing.py                                                    | Selects clades of interest from trees using taxonomic specifications               | Phylogenetic trees                                                         |
+
+# Using the Utilities (in progress of drafting)
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