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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

FastML Source code


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. Downloading and compiling the program
2. Usage

Downloading and compiling the program:
Current version is from January 2014.
Follow these steps to compile the program under unix system:
Run the Perl script: FastML.v3.11/www/fastml/
(Note that you cannot move this script from of its directory, because it uses relative paths to other files in other directories. Sorry)
FastML uses flags in the command line arguments: (for help, type: "perl FastML.v3.11/www/fastml/")

USAGE: perl FastML.v3.11/www/fastml/ --MSA_File MSA_File --seqType [AA|NUC|CODON] --outDir OUTDIR
Required parameters:

--MSA_File    Input multiple sequence alignment in FASTA format

--seqType    Sequence type may be either of: nuc (nucleotides), aa (amino acids), or codon (nucleotides that will be treated as whole codons)

--outDir    FULL PATH of the output directory where all output files will be created
               (NOTE: EACH RUN must have its UNIQUE outDir. In case the outDir does not exists it will be created automatically)

Optional parameters:

--Tree <phylogenetic tree>

--TreeAlg <NJ | RAxML> - How to reconstruct the tree when a tree is not provided by the user; default=NJ

--SubMatrix <JTT | LG | mtREV | cpREV | WAG | DAYHOFF > amino acid options, the default is JTT.
                  <JC_Nuc | T92 | HKY | GTR> nucleotide options, the default is JC_Nuc.
                  <yang | empiriCodon> codon options, the default is yang.

--OptimizeBL <yes | no> default: yes

--UseGamma <yes | no> default: yes

--Alpha <User provide alpha> (relevant only when UseGamma==yes)
              user alpha parameter of the gamma distribution [if alpha is not given, alpha and branches will be evaluated from the data]

--jointReconstruction <yes | no> default: yes

--indelReconstruction <PARSIMONY|ML|BOTH> - which method is used for indel reconstruction

--indelCutOff <Cutoff for indel vs char> deafult = 0.5

> perl FastML.v3.11/www/fastml/ --MSA_File MSA.aln --outDir /home/MSA.FastML --seqType aa --Tree tree.newick

The program will compute ancestral reconstruction of the amino acid data in the MSA.aln file according the tree file in tree.newick based on the default parameters and output all results to the diretory "MSA.FastML" at the home directory

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