A new version of FASTML is available

FASTML version 2.02


FastML is a program for computing the ancestral amino-acid sequences of a phylogenetic tree.
Current version is from 10.11.2003.
For support and questions please email me: talp@post.tau.ac.il

Download the program (for WINDOWS):
fastml.exe (ver 1.05)

FASTML must be followed be one of the following: (default values are in [])

-h = help
-s seq.txt = The sequence input file name
-t tree.txt = The input tree file name (phylip format)
The default sequence format is phylip. To use sequence input files in other format use the -q option
To change the sequence output format use the -R flag. The following formats are supported: Mase,Molphy,Phylip,Clustal,Fasta
Use the -M option to chose a model. The following models are supported (for amino-acids): DAY, JTT, REV, CPREV, WAG, aaJC [JTT].
For nucleotides, currently only the JC model is supported.

Results are printed for various output files:
-j joint reconstruction output file [jrof.txt]
-k marginal reconstruction output file [mrof.txt]
-p phylip tree file format with internal nodes labels [pin.txt]
-f FASTML tree file format with internal nodes labels [fin.txt]
-e joint probability at each position file [jpf.txt]
-d marginal probabilities of each position, and at each node file [mpf.txt]
If the user tree is not given, the program computes a NJ tree, based on the JC distances.

Here are two sample files:
seq.txt (Mase file format)
tree.txt (Phylip tree file format)
You can try the program by typing rate4site.exe -s seq.txt -Qm -t tree.txt

Source code (C++) for UNIX and LINUX is also available for download here
To compile, unzip all files to one directory, and type: g++ -o rate4site.exe -O3 *.cpp This code is to be used only to compile the FASTML program.
If there are problems with the compilations (occasionally, with old version of g++) - please email me and I'll try to help
To modify the code, or use parts of it for other purposes, a permission is requested. Please contact Tal Pupko at talp@post.tau.ac.il

References for the program:
1. Pupko, T., I. Pe'er., R. Shamir, and D. Graur. 2000. A fast algorithm for joint reconstruction of ancestral amino-acid sequences. Mol. Biol. Evol. 17(6): 890-896. [pdf] [abs]

2. 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]

Here you can find an older version of the program (ver 1.04): FASTML version 1.04
Major updates include mainly improvements in the C++ code, and that in this versions gaps are treated as missing characters.