Provided by: fasttree_2.1.10-2_amd64 bug

NAME

       fasttreeMP  - create phylogenetic trees from alignments of nucleotide or protein sequences
       (openMP version)

DESCRIPTION

       fasttreeMP infers approximately-maximum-likelihood phylogenetic trees from  alignments  of
       nucleotide  or  protein sequences. It handles alignments with up to a million of sequences
       in a reasonable amount of time and memory.

       fasttreeMP is more accurate than PhyML 3 with default settings,  and  much  more  accurate
       than  the  distance-matrix  methods  that  are  traditionally  used  for large alignments.
       fasttreeMP uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide
       evolution  and  the  JTT  (Jones-Taylor-Thornton  1992)  model of amino acid evolution. To
       account for the varying rates of evolution across sites, fasttreeMP uses a single rate for
       each  site (the "CAT" approximation). To quickly estimate the reliability of each split in
       the tree, fasttreeMP computes local  support  values  with  the  Shimodaira-Hasegawa  test
       (these are the same as PhyML 3's "SH-like local supports").

SYNOPSIS

       fasttreeMP protein_alignment > tree

       fasttreeMP -nt nucleotide_alignment > tree

       fasttreeMP -nt -gtr < nucleotide_alignment > tree

       fasttreeMP accepts alignments in fasta or phylip interleaved formats

   Common options (must be before the alignment file):
       -quiet to suppress reporting information

       -nopr to suppress progress indicator

       -log logfile -- save intermediate trees, settings, and model details

       -fastest -- speed up the neighbor joining phase & reduce memory usage

              (recommended for >50,000 sequences)

       -n <number> to analyze multiple alignments (phylip format only)

              (use for global bootstrap, with seqboot and CompareToBootstrap.pl)

       -nosupport to not compute support values

       -intree newick_file to set the starting tree(s)

       -intree1 newick_file to use this starting tree for all the alignments

              (for faster global bootstrap on huge alignments)

       -pseudo to use pseudocounts (recommended for highly gapped sequences)

       -gtr -- generalized time-reversible model (nucleotide alignments only)

       -wag -- Whelan-And-Goldman 2001 model (amino acid alignments only)

       -quote -- allow spaces and other restricted characters (but not ' characters) in

              sequence  names  and  quote  names in the output tree (fasta input only; fasttreeMP
              will not be able to read these trees back in

       -noml to turn off maximum-likelihood

       -nome to turn off minimum-evolution NNIs and SPRs

              (recommended if running additional ML NNIs with -intree)

       -nome -mllen with -intree to optimize branch lengths for a fixed topology

       -cat # to specify the number of rate categories of sites (default 20)

              or -nocat to use constant rates

       -gamma -- after optimizing the tree under the CAT approximation,

              rescale the lengths to optimize the Gamma20 likelihood

       -constraints constraintAlignment to constrain the topology search

              constraintAlignment should have 1s or 0s to indicates splits

       -expert -- see more options

   Detailed usage for fasttreeMP 2.1.4 SSE3:
       fasttreeMP [-nt] [-n 100] [-quote] [-pseudo | -pseudo 1.0]

              [-boot   1000   |   -nosupport]    [-intree    starting_trees_file    |    -intree1
              starting_tree_file]  [-quiet  |  -nopr] [-nni 10] [-spr 2] [-noml | -mllen | -mlnni
              10] [-mlacc 2] [-cat 20 | -nocat] [-gamma]  [-slow  |  -fastest]  [-2nd  |  -no2nd]
              [-slownni]  [-seed  1253]  [-top | -notop] [-topm 1.0 [-close 0.75] [-refresh 0.8]]
              [-matrix Matrix | -nomatrix] [-nj | -bionj] [-wag] [-nt] [-gtr] [-gtrrates ac ag at
              cg ct gt] [-gtrfreq A C G T] [ -constraints constraintAlignment [ -constraintWeight
              100.0 ] ] [-log logfile]

              [ alignment_file ]

              > newick_tree

       or

       fasttreeMP [-nt] [-matrix Matrix | -nomatrix] [-rawdist] -makematrix [alignment]

              [-n 100] > phylip_distance_matrix

              fasttreeMP supports fasta or phylip interleaved alignments  By  default  fasttreeMP
              expects  protein  alignments,   use  -nt  for nucleotides fasttreeMP reads standard
              input if no alignment file is given

   Input/output options:
       -n -- read in multiple alignments in. This only

              works with phylip interleaved format. For example, you can use it with  the  output
              from  phylip's  seqboot.  If  you  use -n, fasttreeMP will write 1 tree per line to
              standard output.

       -intree newickfile -- read the starting tree in from newickfile.

              Any branch lengths in the starting trees are ignored.

       -intree with -n will read a separate starting tree for each alignment.

       -intree1 newickfile -- read the same starting tree for each alignment

       -quiet -- do not write to standard error during normal operation (no progress

              indicator, no options summary, no likelihood values, etc.)

       -nopr -- do not write the progress indicator to stderr

       -log logfile -- save intermediate trees so you can extract

              the trees and restart long-running  jobs  if  they  crash  -log  also  reports  the
              per-site rates (1 means slowest category)

       -quote -- quote sequence names in the output and allow spaces, commas,

              parentheses, and colons in them but not ' characters (fasta files only)

   Distances:
              Default: For protein sequences, log-corrected distances and an

              amino acid dissimilarity matrix derived from BLOSUM45

              or  for nucleotide sequences, Jukes-Cantor distances To specify a different matrix,
              use -matrix FilePrefix or -nomatrix Use -rawdist to turn the log-correction off  or
              to use %different instead of Jukes-Cantor

       -pseudo [weight] -- Use pseudocounts to estimate distances between

              sequences with little or no overlap. (Off by default.) Recommended if analyzing the
              alignment has sequences with little or no overlap.  If the weight is not specified,
              it is 1.0

   Topology refinement:
              By  default,  fasttreeMP  tries  to improve the tree with up to 4*log2(N) rounds of
              minimum-evolution nearest-neighbor interchanges (NNI), where N  is  the  number  of
              unique  sequences,  2 rounds of subtree-prune-regraft (SPR) moves (also min. evo.),
              and up to 2*log(N) rounds of maximum-likelihood NNIs.  Use -nni to set  the  number
              of rounds of min. evo. NNIs, and -spr to set the rounds of SPRs.  Use -noml to turn
              off both min-evo NNIs and SPRs (useful if refining

              an approximately maximum-likelihood tree with further NNIs)

              Use -sprlength set the maximum length of a SPR move (default 10) Use -mlnni to  set
              the  number of rounds of maximum-likelihood NNIs Use -mlacc 2 or -mlacc 3 to always
              optimize all 5 branches at each NNI,

              and to optimize all 5 branches in 2 or 3 rounds

              Use -mllen to optimize branch lengths without ML NNIs Use -mllen -nome with -intree
              to  optimize branch lengths on a fixed topology Use -slownni to turn off heuristics
              to avoid constant subtrees (affects both

              ML and ME NNIs)

   Maximum likelihood model options:
       -wag -- Whelan-And-Goldman 2001 model instead of (default) Jones-Taylor-Thorton 1992 model
              (a.a. only)

       -gtr -- generalized time-reversible instead of (default) Jukes-Cantor (nt only)

       -cat # -- specify the number of rate categories of sites (default 20)

       -nocat -- no CAT model (just 1 category)

       -gamma -- after the final round of optimizing branch lengths with the CAT model,

              report  the  likelihood  under  the  discrete  gamma  model with the same number of
              categories. fasttreeMP uses the same branch lengths but optimizes the  gamma  shape
              parameter and the scale of the lengths.  The final tree will have rescaled lengths.
              Used with -log, this also generates per-site likelihoods for use with  CONSEL,  see
              GammaLogToPaup.pl and documentation on the fasttreeMP web site.

   Support value options:
              By  default,  fasttreeMP  computes  local  support  values  by  resampling the site
              likelihoods 1,000 times and the Shimodaira Hasegawa test. If you specify -nome,  it
              will  compute  minimum-evolution  bootstrap  supports  instead  In either case, the
              support values are proportions ranging from 0 to 1

              Use -nosupport to turn off support values or -boot 100 to use  just  100  resamples
              Use -seed to initialize the random number generator

   Searching for the best join:
              By default, fasttreeMP combines the 'visible set' of fast neighbor-joining with

              local hill-climbing as in relaxed neighbor-joining

       -slow -- exhaustive search (like NJ or BIONJ, but different gap handling)

       -slow takes half an hour instead of 8 seconds for 1,250 proteins

       -fastest -- search the visible set (the top hit for each node) only

              Unlike  the  original  fast  neighbor-joining,  -fastest  updates  visible(C) after
              joining A and B if join(AB,C)  is  better  than  join(C,visible(C))  -fastest  also
              updates  out-distances  in  a  very  lazy  way,  -fastest sets -2nd on as well, use
              -fastest -no2nd to avoid this

   Top-hit heuristics:
              By default, fasttreeMP uses a top-hit list to speed up search Use -notop (or -slow)
              to turn this feature off

              and compare all leaves to each other, and all new joined nodes to each other

       -topm 1.0 -- set the top-hit list size to parameter*sqrt(N)

              fasttreeMP  estimates  the  top m hits of a leaf from the top 2*m hits of a 'close'
              neighbor, where close is defined as d(seed,close) < 0.75  *  d(seed,  hit  of  rank
              2*m), and updates the top-hits as joins proceed

       -close 0.75 -- modify the close heuristic, lower is more conservative

       -refresh 0.8 -- compare a joined node to all other nodes if its

              top-hit  list  is less than 80% of the desired length, or if the age of the top-hit
              list is log2(m) or greater

       -2nd or -no2nd to turn 2nd-level top hits heuristic on or off

              This reduces memory usage and running time but may lead to marginal  reductions  in
              tree quality.  (By default, -fastest turns on -2nd.)

   Join options:
       -nj: regular (unweighted) neighbor-joining (default)

       -bionj: weighted joins as in BIONJ

              fasttreeMP will also weight joins during NNIs

   Constrained topology search options:
       -constraints alignmentfile -- an alignment with values of 0, 1, and -

              Not  all  sequences  need  be  present. A column of 0s and 1s defines a constrained
              split. Some constraints may be violated (see 'violating constraints:'  in  standard
              error).

       -constraintWeight -- how strongly to weight the constraints. A value of 1

              means a penalty of 1 in tree length for violating a constraint Default: 100.0

       For more information, see http://www.microbesonline.org/fasttree/

              or the comments in the source code

              fasttreeMP  protein_alignment  >  tree  fasttreeMP  -nt nucleotide_alignment > tree
              fasttreeMP -nt -gtr < nucleotide_alignment > tree

       fasttreeMP accepts alignments in fasta or phylip interleaved formats

   Common options (must be before the alignment file):
       -quiet to suppress reporting information

       -nopr to suppress progress indicator

       -log logfile -- save intermediate trees, settings, and model details

       -fastest -- speed up the neighbor joining phase & reduce memory usage

              (recommended for >50,000 sequences)

       -n <number> to analyze multiple alignments (phylip format only)

              (use for global bootstrap, with seqboot and CompareToBootstrap.pl)

       -nosupport to not compute support values

       -intree newick_file to set the starting tree(s)

       -intree1 newick_file to use this starting tree for all the alignments

              (for faster global bootstrap on huge alignments)

       -pseudo to use pseudocounts (recommended for highly gapped sequences)

       -gtr -- generalized time-reversible model (nucleotide alignments only)

       -wag -- Whelan-And-Goldman 2001 model (amino acid alignments only)

       -quote -- allow spaces and other restricted characters (but not ' characters) in

              sequence names and quote names in the output tree  (fasta  input  only;  fasttreeMP
              will not be able to read these trees back in

       -noml to turn off maximum-likelihood

       -nome to turn off minimum-evolution NNIs and SPRs

              (recommended if running additional ML NNIs with -intree)

       -nome -mllen with -intree to optimize branch lengths for a fixed topology

       -cat # to specify the number of rate categories of sites (default 20)

              or -nocat to use constant rates

       -gamma -- after optimizing the tree under the CAT approximation,

              rescale the lengths to optimize the Gamma20 likelihood

       -constraints constraintAlignment to constrain the topology search

              constraintAlignment should have 1s or 0s to indicates splits

       -expert -- see more options

       For more information, see http://www.microbesonline.org/fasttree/