Manually curated database of 240 orthologs and their paralogs from 304 eukaryotic taxa. These taxa cover the known diversity of eukaryotes.
Main Workflow tools for:
The preparation of custom databases composed of protein coding genes in lieu of the provided database
Ortholog and paralog “mining” from input proteomes
Evaluating completeness in the database of newly input data
Automated removal of non-homologous sites, alignment, trimming, length filtering and single gene tree construction
Visualization of single gene trees and interactive selection of orthologs, paralogs, and removal of contamination
Generation of final statistics post ortholog selection and contamination removal
Can be subset by user provided thresholds of completeness or by assigned taxonomy
Creation of chimeric taxa for use in phylogenomic analyses
Automated concatenation of phylogenomic matrices
Utilities for:
Alternative genetic code prediction
Compositional bias testing (amino acid re-coding)
The removal of fast evolving sites from a phylogenomic dataset
The removal of fast evolving taxa from a phylogenomic dataset
Detection and removal of the most heterotachious sites in a phylogenomic dataset
Examining the number of occurrences of clades of interest in bootstrap trees
Matrix construction from randomly re-sampled genes from a phylogenomic dataset
Binning single-protein trees based on Relative Tree Certainty (RTC)
Collapsing of multiple proteomes to produce a single “most complete” proteome with regards to the database (useful for single-cell data and to form chimeric taxa from closely related species)
Figure 1: Overview of the PhyloFisher workflow and package contents. The PhyloFisher package consists of a manually curated database of 240 protein coding genes and their paralogs from 304 eukaryotic taxa; a series tools to perform the essential steps of phylogenomic dataset construction (homolog collection, single-protein tree construction, removal of paralogs and contaminants, matrix concatenation); and many pre and post-construction analyses necessary for a publication-quality phylogenomic study.
