HandelPackage < Main

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HandelPackage

Handel: an evolutionary model-based StatisticalAlignment package.

Main program:
- handalign - program to sample multiple alignments, phylogenies, and parameters. Currently the main supported program in the Handel package. See HandAlign transducer for a depiction of the underlying model.
  - Input:
    - either unaligned sequences (FastaFormat), or (optionally) an alignment (StockholmFormat) which may include an embedded tree (NewickFormat)
    - optional rate matrix (XrateFormat)
  - Output:
    - final or best alignment (StockholmFormat) with embedded tree (NewickFormat) and model parameters
    - (optionally) an MCMC sampling trace of all alignments/trees/parameters visited (StockholmFormat + NewickFormat)
Utility programs:
- StockholmTools - utilities for working with files in StockholmFormat
- phylocomposer - program for analysis using StringTransducers. Can be used to reproduce the individual sampling steps of handalign.
  - Input: tree, transducer composition file (PhyloComposer format -- a derivative of Lisp S Expressions)
  - Output: composite & acyclic transducers, alignments (PhyloComposer format)
- phylodirector.pl - program for visualizing state paths through StringTransducers
  - Input: alignment (StockholmFormat)
  - Output: movie file (MPEG Format); still image files (PNG Format & SVG Format)
Older programs in the package:
- tkfemit - program to sample multiple alignments from the prior implied by the TKF91 model and a given phylogenetic tree
  - Input: tree (NewickFormat), optional rate matrix (XrateFormat)
  - Output: alignment (StockholmFormat)
- tkfdistance - program to estimate distance matrices using the TKF91 model
  - Input: either sequences (FastaFormat) or an alignment (StockholmFormat)
  - Output: distance matrix (DistanceFormat)
- tkfalign - MCMC phylogenetic alignment package using TKF91
  - Input: tree (NewickFormat), optional rate matrix (XrateFormat), and either sequences (FastaFormat) or an alignment (StockholmFormat)
  - Output: alignment(s) (StockholmFormat)
  - See WhyMCMCIsNetworkingForModelers for discussion of why the MCMC functionality is cool

Related programs in DART...

StemLoc, EvolDoer: multiple alignment of RNA
- Input: either sequences (FastaFormat) or alignments (StockholmFormat)
- Output: alignment(s) (StockholmFormat)

xrate: mutation rate measurement using EM algorithm (XrateFormat, StockholmFormat)
xfold, xprot and xgram: multiple alignment annotation using evolutionary SCFGs (XgramFormat, StockholmFormat)

Background...

See PhylogeneticAlignmentReader for more background info and context on PhyloAlignment
- a good review is Lunter G, Miklos I, Drummond A, Jensen JL, Hein J. Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics. 2005 Apr 1;6:83.
See MultipleRNAAlignment for papers and theory relating to multiple alignment of RNA

Getting in touch...

Topic revision: r47 - 2011-12-26 - IanHolmes