FastML Source code

Overview

1. Download the FastML code archive.
2. In order to unzip and untar the files, please type:


tar -xzf FastML.v3.11.tgz

This will create the directory FastML.v3.11
3. Compile the package by typing:

cd FastML.v3.11
make

(Running 'make' takes a while, warnnings issued can be ignored)
4A. FastML uses Perl: Type "perl -v" and check that Perl is installed.

If it's not installed, download and install it from: http://www.perl.org/
4B. To use RAxML algorithm to reconstruct the phylogentic tree during FastML run (optional), RAxML and BioPerl should be installed in your system.
RAxML: Type "which raxmlHPC" and check that the program is found

If it's not installed, download and install RAxML from: http://sco.h-its.org/exelixis/web/software/raxml/index.html
BioPerl: Type "perl -e 'use Bio::SeqIO'" to check that BioPerl is installed.

If it's not installed, download and install it from: http://www.bioperl.org/

USAGE: perl FastML.v3.11/www/fastml/FastML_Wrapper.pl --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

EXAMPLE:
> perl FastML.v3.11/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.