This repository provides some additional functionality to fastml to allow it to work with Gubbins. The original code is available from http://fastml.tau.ac.il/source.html and should be your first port of call.
In citing the FASTML server please refer to:
Ashkenazy H, Penn O, Doron-Faigenboim A, Cohen O, Cannarozzi G, Zomer O, Pupko T. 2012 FastML: a web server for probabilistic reconstruction of ancestral sequences Nucleic Acids Res. 40(Web Server issue):W580-4. [pdf] [abs]
Pupko T, Pe'er I, Hasegawa M, Graur D, Friedman N. 2002 A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families. Bioinformatics 18(8): 1116-1123. [pdf] [abs]
Pupko T, Pe'er I, Shamir R, Graur D. 2000. A fast algorithm for joint reconstruction of ancestral amino-acid sequences. Mol. Biol. Evol. 17(6): 890-896. [pdf] [abs]
Pupko, T. and Pe'er I. 2000. Maximum likelihood reconstruction of ancestral amino-acid sequences. Currents in Computational Molecular Biology. Ed. Miyano, S., Shamir, R, and Takagi, T. pp. 184-185. Universal Academy Press, Tokyo, Japan. [pdf]
We're working on tarball source relases from upstream. As such it is difficult to maintain a sensible change history over time. Essentially, we have a set of source changes (that can't be represented as a clean patch) that are applied to each release of FastML.
Aidan Delaney Tue Apr 08 2014
- Partial port of v2.02 changes to v3.1.
Andrew Page Fri Sep 28 2012
- Initial source changes on top of version 2.02.