Handel: an evolutionary model-based Statistical Alignment package.
- Main program:
* final or best alignment (Stockholm Format) with embedded tree (Newick Format) and model parameters * (optionally) an MCMC sampling trace of all alignments/trees/parameters visited (Stockholm Format + Newick Format)
- Utility programs:
- Stockholm Tools - utilities for working with files in Stockholm Format
- phylocomposer - program for analysis using String Transducers. Can be used to reproduce the individual sampling steps of handalign.
- phylodirector.pl - program for visualizing state paths through String Transducers
- Older programs in the package:
- tkfemit - program to sample multiple alignments from the prior implied by the TKF91 model and a given phylogenetic tree
- tkfdistance - program to estimate distance matrices using the TKF91 model
- tkfalign - MCMC phylogenetic alignment package using TKF91
Related programs in DART...
- StemLoc, Evol Doer: multiple alignment of RNA
- xrate: mutation rate measurement using EM algorithm (Xrate Format, Stockholm Format)
- xfold, xprot and xgram: multiple alignment annotation using evolutionary SCFGs (Xgram Format, Stockholm Format)
- See Phylogenetic Alignment Reader for more background info and context on Phylo Alignment
- a good review is Lunter et al.: Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics 2005;6:83.
- See Multiple RNAAlignment for papers and theory relating to multiple alignment of RNA
Getting in touch...