GenNon-H generates MSAs evolving under discrete-time Markov processes on phylogenetic trees, directly from probability substitution matrices. Based on the input model and a phylogenetic tree in the Newick format (with branch lengths measured as the expected number of substitutions per site), the algorithm produces DNA alignments of desired length. GenNon-h outputs nonstationary or non-homogeneous phylogenetic data that is well suited for testing complex biological hypotheses, exploring the limits of the reconstruction algorithms and their robustness to such models.

The package used version 1.47.0 of the boost library for parts of the code involving maths and random generation (downloaded from: boost source). As such, use, modification and distribution are subject to the Boost Software License, Version 1.0. (See boost license).

To compile this code you need a development environment with the GNU gcc compiler ('make'). The following command simulates [fasta] alignments of a given length with random parameters for a given model (jc, k80, k81, ssm, gmm) and tree topology:

GenNon-h <tree file> <output file name> <length> <model>.

Branch lengths should be included in the Newick format within the tree file. The parameters used for the simulations will be saved in a file of the same basename as the output and ".dat” suffix.

./GenNon-h test.nw data.fa 50000 jc

Model: Kimura 81
Tree:
nodes:   7
nleaves: 5
nedges:  6
Edges:
  (5, 6)  0.5
  (5, 3)  0.4
  (5, 4)  0.7
  (6, 0)  0.01
  (6, 1)  0.2
  (6, 2)  0.3

The nodes are labeled in the following order: first the leaves (edges leading to the cherries), then the top-down search starting from the node labeled as the root (the node of highest depth), proceeding left to right as indicated in the Newick format.

Fasta MSA (.fa) and parameters used for the simulations (.dat): Line 1: # of leaves, # of edges, Line 2: equilibrium frequencies of a node chosen as the root

Output matrices are listed acc. to the order outlined above:

1. matrices are first assigned to the leaf edges (bottom branches)
2. top-down left to right branch order.

Kedzierska A.M. and Casanellas M.: “ GenNon-h: Simulating multiple sequence alignments under the non-homogeneous dna models “, BMC Bioinformatics 2012, 13:216.

For methods of parameter estimation of non-homogeneous alignments:

Kedzierska A.M. and Casanellas M.: “ EM for parameter estimation of Markov models on trees ” (revision).