||The FASTML Server
Server for computing Maximum Likelihood
ancestral sequence reconstruction
USAGE: fastML.exe parameterFileRequired parameters:parameterFile FastML parameter fileAbout 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 TalP@post.tau.ac.il.
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 https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html.
For any problems or questions please contact us at bioSequence@tauex.tau.ac.il.