StatAlign is an extendable software package for Bayesian analysis of protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable quantification of the uncertainty in these estimates.Read more about StatAlign
WeaveAlign is a framework for combining a collection of multiple sequence alignments into a directed acyclic graph (DAG) structure, so as to permit efficient inference on very large sets of possible alignments.
Due to interchanges and crossovers in the DAG, the number of alignments encoded in the graph is typically many orders of magnitude greater than the number of alignment samples used to generate the DAG, such that the effective sample size is greatly increased by this representation. Read more about WeaveAlign