Addtional functionality for fastml, see http://fastml.tau.ac.il
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Readme.md

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. To modify the original code, or use parts of it for other purposes, permission should be requested. Please contact Tal Pupko: talp@post.tau.ac.il

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
./configure
make
make install

#To install on Ubuntu (trusty):

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