||The FASTML Server
Server for computing Maximum Likelihood
ancestral sequence reconstruction
tar -xzf FastML.v3.1.tgzThis will create the directory FastML.v3.1 3. Compile the package by typing:
cd FastML.v3.1(Running 'make' takes a while, warnnings issued can be ignored) 4A. FastML uses Perl: Type "perl -v" and check that Perl is installed.
USAGE: perl FastML.v3.1/www/fastml/FastML_Wrapper.pl --MSA_File MSA_File --seqType [AA|NUC|CODON] --outDir OUTDIRRequired 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 createdOptional parameters:
(NOTE: EACH RUN must have its UNIQUE outDir. In case the outDir does not exists it will be created automatically)--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.v3.1/www/fastml/FastML_Wrapper.pl --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
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.