Addtional functionality for fastml, see
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This repository provides some additional functionality to fastml to allow it to work with Gubbins. The original code is available from and should be your first port of call. To modify the original code, or use parts of it for other purposes, permission should be requested. Please contact Tal Pupko:

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]

#To install from source:

autoreconf -i
make install

#To install on Ubuntu (trusty):

sudo apt-get-repository ppa:ap13/gubbins
sudo apt-get update
sudo apt-get install fastml2