From e6217e5d07785009a0122749e8bb0f756eace640 Mon Sep 17 00:00:00 2001 From: Katzlab Date: Fri, 9 Aug 2024 15:03:08 -0400 Subject: [PATCH] Updated Home (markdown) --- Home.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/Home.md b/Home.md index 9a3c805..abad927 100644 --- a/Home.md +++ b/Home.md @@ -1,12 +1,9 @@ -# Overview: PhyloToL version 6 is designed to be a modular, accessible pipeline that includes sophisticated data curation methods, including a newly designed method of phylogeny-informed contamination removal, gene families homology estimation, and generation multisequence alignments (MSAs) and gene trees. The core PhyloToL pipeline comprises two main components, which we refer to as PhyloToL parts I and II. PhyloToL 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. 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), 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. We also provide a suite of utility scripts for describing data output by PhyloToL (e.g. basic sequence statistics such as composition, coverage, and length) as well as performing some of PhyloToL's more complex operations (e.g. "clade-grabbing") in a stand-alone form. -# Table of Contents - ## PhyloToL Part 1 * [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/PTL1-Overview) * [Set up](https://github.com/Katzlab/PhyloToL-6/wiki/Set-up)