Utilities summary

EukPhylo includes a set of stand-alone utility scripts that aim to increase the power of the analysis done with or without the core EukPhylo pipeline. We divide these scripts into five main categories: assembly and fasta tools, sequence composition, MSA tools, gene tree descriptions and stand alone clade grabbing.

assembly and fasta tools capture tasks including downloading sequences from GenBank, clustering sequences, calculating statistics on assemblies, and estimating most shared gene families (OGs) for use in EukPhylo part 2
sequence composition analysis calculates statistics for coding domains (e.g. composition, effective number of codons), plots outputs, and enables users to rename sequences in "ready to gos" based on GC content at silent sites.
MSA tools include assessment of gaps, a wrapper for Guidance analyses, and a tool to count taxa across gene families (useful for deciding on which trees to run after part 1
Gene tree description utilities allows users to modify trees (i.e. to rename and color tips) and to assess clade sizes and levels of contamination
Stand-alone clade grabbing allows users to select sequences from robust clades based on user defined rules

All utilities are written in Python and contain headers that provide information on usage, and a summary of utilities is divided by category here

Category	Script name	Intent	Output
Assembly and fasta tools	Assess_transcriptomes.py	Calculates the length, GC content, and coverage of assembled files	Spreadsheet containing the length, coverage, and GC of each transcript.
	Cluster.py	Clusters sequences in a fasta file	Clustered fasta files
	GetTaxonomy.py	Collects taxonomic classification of organisms from NCBI	Spreadsheet with NCBI taxonomy
	GetUniqueTaxa.py	Gets the unique taxa from a taxonomic classification	Spreadsheet with unique taxa
	Plot_transcriptomes.py	Plots the length, coverage, and GC distribution of transcriptomes.	Plots of transcripts distribution.
	QuerySRA.py	Downloads assemblies from NCBI	Assemblies, IDs, and GCA or SRR codes.
	ReadMapping.py	Maps a group of trimmed reads to a reference	Sam/Bam files.
	SeqLenToCsv.py	Calculates the length of DNA sequences in fasta files	Spreadsheet containing the length of all sequences.
	SharedOGs.py	Summarizes the gene family presence in fasta files	Spreadsheet with the gene families

Sequence composition analysis	CUB.py	Summarizes the nucleotide composition of fasta files	Fasta file and several spreadsheets summarizing the nucelotide composition
	GC_identifier.py	Renames sequence ID by GC composition	Fasta files with relabeled sequence ID
	PlotComps.r	Produces GC3 width plots	GC3 width plots
	Plotcomps_SppName.R	Produces GC3 width plots with the species name and # seqs added to each plot	GC3 width plots

MSA tools	BacktranslateAlignment.py	Produces new nucleotide alignment from an amino acid alignment	Aligned nucelotide file
	CountTaxonOccurence.py	Counts the occurences of each taxa in each gene family of a post guidance file	Spreadsheet with counts of taxa
	friendlessness.py	Describes the internal regions of insertion unique or nearly unique to a sequence	Spreadsheet with each sequence statistics
	Gappiness.py	Produces statistics on the terminal and internal gaps of an alignment	Spreadsheet with the paralogs statistics
	GuidanceWrapper.py	Guidance wrapper that can be used in place of EukPhylo pipeline	Guidanced alignment files

Gene tree description	CladeSizes.py	Describes clade sizes for different taxonomic groups	Spreadsheet describing clade sizes
	ColorByClade.py	Visualizes placement of taxa by taxonomic group in trees	Colored trees
	ContaminationBySisters.py	Summarizes the taxonomic distribution of sister sequences for each taxon in a tree	Two spreadsheets summarizing tree tips relationship
	RenameTips.py	Renames the tip labels of trees to include metadata such as location and date	Renamed trees

Stand-alone clade grabbing	CladeGrabbing.py	Selects clades of interest from trees using taxonomic specifications	Phylogenetic trees

Using the Utilities (in progress of drafting)