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The FASTML Server
Server for computing Maximum Likelihood
ancestral sequence reconstruction

The FASTML Server - Server for computing Maximum Likelihood ancestral sequence reconstruction - Source code

New FastML Program


The FastML server is a bioinformatics tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences. The server runs several algorithms that reconstruct the ancestral sequences with emphasis on an accurate reconstruction of both indels and characters (see Overview). When citing the program, please use the same references as for the FastML web-server.

* Please note that dataset size is limited to 200 sequences.

1. Download the FastML windows executable or Linux executable
2. Usage

USAGE: fastML.exe parameterFile
Required parameters:

parameterFile    FastML parameter file

About Parameter file:

Download Example parameter file.

The following are the parameters used by the parameter file:


treefile - Tree file address (newick format)

seqfile - Multiple sequence alignment file address (fasta format)


Modelweightsfile - Weight file to be used only with the MIX model (see example)

   Download Example weight file.

outTreeFileNewick - Output tree (Newick format)

outTreeFileAncestor - Ancestor file that names the internal nodes

outFile_prob_joint - Likelihood file for joint reconstruction

outFile_prob_marginal - Likelihood file for marginal reconstruction

outFile_seq_joint - joint reconstruction sequences

outFile_seq_marginal - Marginal reconstruction sequences

reportFile - Run report (contains error report if any occured)

seqOutputFormat - Sequence output format fasta/mase/clustal/molphy/phylip/nexus

distributionName - Rate variation distribution hom/gam (homogenic/gamma)

boundMethod - max/sum/both used for the joint reconstruction with gamma distribution

(for more information regarding this parameter see: "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." Pupko T. et al)

modelName - model name DAY(Dayhoff)/LG/JTT/REV/CPREV/WAG/HKY/TAMURA92/NYCODON/NUCJC/AAJC/EMPIRICODON/MIX(new model, uses weight file)

gammaCategies - Number of district categories for the gamma distribution

optimizeBrLenOnStartingTree - 1/0 (yes/no) optimization of branch length of the tree

Copyright (C) 2012 Tal Pupko

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see

For any problems or questions please contact us at