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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. More details can be found in the manuscript files here (**TBD insert BioRxiv link**) EukPhylo version 1.0 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 (pending publication)
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. 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.
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. 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.
## PhyloToL Part 1 – Gene family assignment ## EukPhylo Part 1 – Gene family assignment
* [Overview and modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1:-gf-assignment#overview-and-modularity) * [Overview and modularity](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-1:-gf-assignment#overview-and-modularity)
* [Setup](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1:-gf-assignment#setup) * [Setup](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-1:-gf-assignment#setup)
* [The Hook Database](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1:-gf-assignment#the-hook-database) * [The Hook Database](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-1:-gf-assignment#the-hook-database)
* [Running PhyloToL Part 1](https://github.com/Katzlab/PhyloToL-6/wiki/PhyloToL-Part-1:-gf-assignment#running-phylotol-part-1) * [Running EukPhylo Part 1](https://github.com/Katzlab/EukPhylo/wiki/PhyloToL-Part-1:-gf-assignment#running-phylotol-part-1)
* [Processing transcriptomes](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-1:-gf-assignment#processing-transcriptomes) * [Processing transcriptomes](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-1:-gf-assignment#processing-transcriptomes)
* [Processing genomes](https://github.com/Katzlab/PhyloToL-6/wiki/Part1phylotol-part-1:-gf-assignment#processing-genomes) * [Processing genomes](https://github.com/Katzlab/EukPhylo/wiki/Part1phylotol-part-1:-gf-assignment#processing-genomes)
## PhyloToL Part 2 – MSAs, gene trees, and contamination loop ## EukPhylo Part 2 – MSAs, gene trees, and contamination loop
* [Overview and modularity](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#overview-and-modularity) * [Overview and modularity](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#overview-and-modularity)
* [Setup](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#setup) * [Setup](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#setup)
* [Databases](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#databases) * [Databases](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#databases)
* [Running PhyloToL Part 2](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop) * [Running PhyloToL Part 2](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop)
* [Overlap and similarity filters](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#overlap-and-similarity-filters) * [Overlap and similarity filters](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#overlap-and-similarity-filters)
* [Guidance](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#guidance) * [Guidance](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#guidance)
* [Gene trees](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#gene-trees) * [Gene trees](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#gene-trees)
* [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/PhyloToL-6/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#contamination-loop) * [Contamination loop: phylogeny-informed contamination removal](https://github.com/Katzlab/EukPhylo/wiki/phylotol-part-2:-MSAs,-trees,-and-contamination-loop#contamination-loop)
## Other ## Other
* [Utility scripts](https://github.com/Katzlab/PhyloToL-6/wiki/Utilities) * [Utility scripts](https://github.com/Katzlab/EukPhylo/wiki/Utilities)
* [Troubleshooting and FAQs](https://github.com/Katzlab/PhyloToL-6/wiki/Troubleshooting_FAQs) * [Troubleshooting and FAQs](https://github.com/Katzlab/EukPhylo/wiki/Troubleshooting_FAQs)
* [FAQs](https://github.com/Katzlab/PhyloToL-6/wiki/TroubleShooting-&-FAQs#faqs) * [FAQs](https://github.com/Katzlab/EukPhylo/wiki/TroubleShooting-&-FAQs#faqs)