From 25b3665f36aca9e23c4efe4099bd0ef3d810ef48 Mon Sep 17 00:00:00 2001
From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com>
Date: Fri, 18 Apr 2025 08:46:38 -0400
Subject: [PATCH] Updated Home (markdown)

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@@ -2,8 +2,6 @@ EukPhylo version 1.0 is designed to be a modular, accessible pipeline that inclu
 
 The core EukPhylo pipeline comprises two main components, which we refer to as EukPhylo parts 1 and 2. EukPhylo part 1 takes input sequences from a whole genome or transcriptome assembly, applies several curation steps, and provides initial homology assessment against a customizable database of reference sequences to assign GFs. Part one outputs a fasta file of curated nucleotide and amino acid sequences with gene families assigned, as well as a dataset of descriptive statistics (e.g. length, coverage, and composition) for each input sample. EukPhylo part 2 is highly modular; for a given selection of taxa and GFs it stringently assesses homology by iterating the tool Guidance (Penn et al., 2010; Sela et al., 2015), which outputs an MSA for each gene family. From MSAs it builds gene trees, and then includes an innovative workflow for tree topology-based contamination removal. 
 
-Note that we initially developped EukPhylo with Guidance v2.0.2, and then updated the pipeline with the newest version (Guidance v1), some changes in the script might be necessary if users are using the first or second version of the tool.
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 We also provide a suite of utility scripts for describing data output by EukPhylo (e.g. basic sequence statistics such as composition, coverage, and length) as well as performing some of EukPhylo's more complex operations (e.g. "clade-grabbing") in a stand-alone form.
 
 Note that EukPhylo used to go by the name of "PhyloToL," hence some residual instances where we refer to "PTL1" and "PTL2" instead of "EukPhylo part 1" and "EukPhylo part 2" respectively (for instance, in the Github folder structure).