A new version of FASTML is available

FASTML version 2.02

---

FASTML (VERSION 1.04)

FastML is a program for computing the ancestral amino-acid sequences of a phylogenetic tree.
Version 1.04 is from 27.3.2001.
For support and questions please email me: talp@post.tau.ac.il


DownLoad the program (for WINDOWS):
fastml.exe (ver 1.04)

Sample files:
seq.txt (Mase file format)
tree.txt (Phylip tree file format)

Usage:
FastML must be followed be one of the following: [ stands for default value ]

-aa = amino-acid [aa]
-sfn seq.txt = seqinputfile.txt is the sequence input file name [seq.txt]
-mase -paml -phylip -clustal -fasta = sequence file format [mase]
-2mase -2paml -2phylip -2clustal -2fasta = sequence output file format [mase]
-tfn ppp = ppp is the input tree file name (phylip format) [tree.txt]
-f = frequencies are taken from the data [no minus f]
-jtt or -day or -rev = the matrix; [JTT]
-exact = don't use the chebyshev approximation [use cheby]
-approx = use chebyshev [use cheby]
-chebNumCoef 13 = 13 coefficient are used in the chebyshev series [13]
-jrof jjj = jjj is the joint reconstruction output file [jrof.txt]
-mrof hhh = hhh is the marginal reconstruction output file [mrof.txt]
-pin nnn = nnn is a phylip tree file with internal nodes labels [pin.txt]
-fin mmm = mmm is a fastml format file with internal nodes
-jpf xxx = xxx is the joint-probability-of-each-position file [jpf.txt]
-interactive = interactive input/output for the program


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]