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# Overview: # Overview:
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), 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. 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.
We also provide 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 # Table of Contents
## PhyloToL Part I = determining gene families ## PhyloToL Part 1
* Overview * [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/PTL1-Overview)
* [Set up](https://github.com/Katzlab/PhyloToL-6/wiki/Set-up) * [Set up](https://github.com/Katzlab/PhyloToL-6/wiki/Set-up)
* The Hook reference database for gene family assigment * [The Hook Database](https://github.com/Katzlab/PhyloToL-6/wiki/Hook)
* [Processing transcriptomes](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.masnnqe0fycn) * [Processing transcriptomes](https://github.com/Katzlab/PhyloToL-6/wiki/Processing-transcriptomes)
* [Processing genomes](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.15uyieg4qumy) with CDs * [Processing genomes](https://github.com/Katzlab/PhyloToL-6/wiki/Processing-genomes)
* [Starting at different points in the process](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.sjrzmygryaj4) (Folder structure)
## PhyloToL Part 2 = generating MSAs and gene trees ## PhyloToL Part 2
* Overview of the process * [Overview & modularity](https://github.com/Katzlab/PhyloToL-6/wiki/PTL2-Overview)
* Producing and curating MSAs * [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/pre-Guidance)
* Filtering by composition * [Guidance](https://github.com/Katzlab/PhyloToL-6/wiki/Guidance)
* [Building gene trees](https://docs.google.com/document/d/1pXMPZwK17yfk5-kIGYzwTSTO-5ggoMq-5II16nAPWAo/edit#heading=h.5f0xducehljc) * [Building gene trees](https://github.com/Katzlab/PhyloToL-6/wiki/Trees)
* Contamination loop: phylogeny-informed contamination removal * [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/PhyloToL-6/wiki/Contamination-loop)
## Utilities ## Other
* [Utility scripts](https://github.com/Katzlab/PhyloToL-6/wiki/Utilities)
## Troubleshooting Guide * [Troubleshooting](https://github.com/Katzlab/PhyloToL-6/wiki/Troubleshooting)
## Appendices