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-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 generating multisequence alignments (MSAs) and gene trees.
+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 generating multisequence alignments (MSAs) and gene trees. More details can be found in the manuscript files here (**TBD insert BioRxiv link**)
 
 The core PhyloToL pipeline comprises two main components, which we refer to as PhyloToL parts 1 and 2. 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.