Software

PhyloWGA: phylogenetic analyses and interrogation of whole genome alignments (WGAs)

Github Page: https://github.com/radamsRHA/PhyloWA

  • Examples/Citations: Adams et al., 2020, Bioinformatics 
  • Software: PhyloWGA (written by Rich Adams) 
  • Description: PhyloWGA: a user-friendly framework for chromosome-aware phylogenetic interrogation of whole genome alignments.

GppFst: Genomic posterior predictive simulations of Fst and dXY for identifying outlier loci from population genomic data.

Github Page: https://github.com/radamsRHA/GppFst

  • Examples/Citations: Adams et al., 2016, Bioinformatics 
  • Software: GPPFst (written by Rich Adams) 
  • Description: GppFst is an open source R package that generates posterior predictive distributions of Fst and dXY under a neutral coalescent model to identify putative targets of selection from genomic data.

ThetaMater: Bayesian estimation of population size parameter θ from genomic data.

Github Page: https://github.com/radamsRHA/ThetaMater

  • Examples/Citations: Adams et al., 2017, Bioinformatics 
  • Software: ThetaMater (written by Rich Adams) 
  • Description: ThetaMater is an open source R package comprising a suite of functions for efficient and scalable Bayesian estimation of the population size parameter θ from population genomic data.

pSTDistanceR: computing probabilistic distances between species tree models under the multispecies coalescent.

Github Page: https://github.com/radamsRHA/PSTDistanceR

  • Examples/Citations: Adams and Castoe, 2019, Systematic Biology
  • Software: pSTDistanceR (written by Rich Adams) 
  • Description: pSTDistanceR is an open source R package comprising a suite of functions for computing probabilistic distances between species tree models using the equations provided in Adams and Castoe, 2019. 

Analysis & identification of microsatellite loci from shotgun next-generation reads

  • Examples/Citations: Castoe et al., 2010, MER; Castoe et al., 2012, PLoS ONE 
  • Software: pal_finder_v2.3 (written by Alex Poole 
  • Description: This is a script to identify and characterize microsatellite repeat loci from shotgun genomic sampling by 454 or Illumina paired-end reads, and design PCR primers flanking these loci. It requires a local install of Primer3 for the primer-design phase. 
  • UPDATE: pal_finder_v0.02.04b (written by Alex Poole; Please cite Castoe et al., 2012, PLoS ONE).
    • Description: Updated to handle Illumina HiSeq scarf headers and FastQ input files…

Analyses of Convergent Molecular Evolution

  • Examples/Citations: Castoe et al., 2009, PNAS 
  • Software: codeml ancestral (written by Jason de Koning 
  • Description: Modified version of Yang’s PAML codeml package designed to calculate the expected convergent substitutions while integrating over uncertainty in the ancestral state estimates.

Evolutionary analysis of complex models of nucleotide and protein evolution, so fast it will make your head spin!!! a.k.a. Phylogenetics, Likelihood, Evolution, and compleXity - PLEX

  • Examples/Citations: de Koning et al., 2009, MBE; deKoning et al., 2012, Bioinformatics
  • Software: PLEX (written by Jason de Koning)
  • Description: This is broad and flexible analysis platform designed to utilize a broad spectrum of complex models and approaches to analyze large phylogenetic datasets, extremely rapidly. At this point, note that this software is not designed to conduct phylogenetic searches (at least, per se), but instead mostly devoted to the analysis and testing of complex models of nucleotide and protein evolution for the purposes of molecular evolutionary analysis.