Updated Home (markdown)

Home.md

@@ -1,11 +1,8 @@
 # Overview:
-PhyloToL is… 
+The core PhyloToL pipeline comprises two main components, which we refer to as PhyloToL part one and part two. PhyloToL part one 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. PhyloToL 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)](https://www.zotero.org/google-docs/?Du5DgO), 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. In addition to presenting the core pipeline and accompanying utility scripts, we describe the results of an analysis of 500 conserved GFs using PhyloToL, from which we remove contamination and construct species trees.
 
 # Table of Contents
 
-
-## Introduction
-
 ## PhyloToL Part I = determining gene families
 * Overview
 * [Set up](https://github.com/Katzlab/PhyloToL-6/wiki/Set-up)