NAME

       fastml - maximum likelihood ancestral amino-acid sequence reconstruction

SYNOPSIS

       fastml [options]

DESCRIPTION

       FastML  is  a bioinformatics tool for the reconstruction of ancestral sequences based on the phylogenetic
       relations between homologous sequences. FastML runs several algorithms  that  reconstruct  the  ancestral
       sequences  with  emphasis  on  an  accurate  reconstruction  of both indels and characters. For character
       reconstruction the previously described FastML algorithms are used to efficiently infer the  most  likely
       ancestral  sequences  for each internal node of the tree. Both joint and the marginal reconstructions are
       provided. For indels reconstruction the sequences are first coded according to the indel events  detected
       within  the  multiple  sequence  alignment  (MSA) and then a state-of-the-art likelihood model is used to
       reconstruct ancestral indels states. The results are the most probable sequences, together with posterior
       probabilities for each character and indel at each sequence position for each internal node of the  tree.
       FastML  is  generic  and is applicable for any type of molecular sequences (nucleotide, protein, or codon
       sequences).

OPTIONS

       -h     help

       -s     sequence input file (for example use -s emySequences/eseq.txt)

       -t     tree input file (if tree is not given, a neighbor joining tree is computed).

       -g     Assume among site rate variation model (Gamma) [By default the program
              will assume an homogeneous model. very fast, but less accurate!]

       -m     model name

       -mj    [JTT]

       -ml    LG

       -mr    mtREV (for mitochondrial genomes)

       -md    DAY

       -mw    WAG

       -mc    cpREV (for chloroplasts genomes)

       -ma    Jukes and Cantor (JC) for amino acids

       -mn    Jukes and Cantor (JC) for nucleotides

       -mh    HKY Model for nucleotides

       -mg    nucgtr Model for nucleotides

       -mt    tamura92 Model for nucleotides

       -my    yang M5 codons model

       -me    empirical codon matrix

       Controling the output options:

       -x     tree file output in Newick format [tree.newick.txt]

       -y     tree file output in ANCESTOR format [tree.ancestor.txt]

       -j     joint sequences output file [seq.joint.txt]

       -k     marginal sequences output file [seq.marginal.txt]

       -d     joint probabilities output file [prob.joint.txt]

       -e     marginal probabilities output file [prob.marginal.txt]

       -q     ancestral sequences output format. (-qc = [CLUSTAL], -qf = FASTA,
              -qm = MOLPHY, -qs = MASE, -qp = PHLIYP, -qn = Nexus)

       Advanced options:

       -a     Threshold for computing again marginal probabilities [0.9]

       -b     Do not optimize branch lengths on starting tree
              [by default branches and alpha are ML optimized from the data]

       -c     number of discrete Gamma categories for the gamma distribution [8]

       -f     don't compute Joint reconstruction (good if the branch and bound algorithm takes  too  much  time,
              and the goal is to compute the marginal reconstruction with Gamma).

       -z     The bound used. -zs - bound based on sum. -zm based on max. -zb [both]

       -p     user  alpha parameter of the gamma distribution [if alpha is not given, alpha and branches will be
              evaluated from the data (override -b)

fastml.sh 3.1                                     November 2015                                     FASTML.SH(1)