File manipulation and conversion is a tedious and error-prone, but often required, component of phylogenetic analysis, made more burdensome by the volume of data available in current phylogenomics studies. phyx supports the popular formats for sequence alignments (fasta, fastq, phylip and Nexus) and trees (newick and Nexus), and provides lightweight, high-throughput utilities to convert data among formats without the user needing to provide the format of the original data as phyx will attempt to auto-detect the original format. Alignments can be further manipulated by removing individual taxa, resampling (bootstrap or jackknifing), sequence recoding, translation to protein, reverse complementation, filtering by quality scores or the amount of missing data, and concatenation across mixed alignment formats.
Processing large data matrices is only one step required for phylogenomic analyses. In order to perform downstream analyses (e.g. orthology detection (Yang and Smith, 2014 (link)), mapping gene trees to species tree (Smith et al., 2015 (link)), or gene tree/species tree reconciliation (Mirarab et al., 2014 (link))) it is now also essential to be able to manipulate individual gene trees constructed from these data. phyx enables fast, efficient manipulations such as pruning individual taxa, extracting subclades and rerooting/unrooting trees. Finally, Bayesian MCMC analyses involving phylogenies have become common in the biological sciences, and often involve large log files generated from replicated analyses. phyx enables both the concatenation and resampling (burnin and/or thinning) of MCMC tree or parameter logs for downstream summary.